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CGD News Archive

2015 CGD News Archive

 

Updates to C. glabrata genome annotation

Multiple C. glabrata gene models were updated based on gene expression analysis conducted by Linde et al. (2015). 4,994 features were affected: 107 new features were added, including 49 protein-coding genes and 58 non-coding RNAs; 4 ORFs were deleted; the sequences for 132 features were extended and 10 shortened; 15 features were split to create 35 new features; 2 features were merged to create 1 new feature; 4,819 5-prime UTRs and 4,828 3-prime UTRs were added; The intron/exon structure was modified for 60 features; splice variants were identified for 16 features. For a list of updates, see Supplementary Table. (Posted April 15, 2015)

2014 CGD News Archive

 

CGD Grant Renewal and Survey

Our renewal of CGD's R01 grant was unsuccessful, so we are currently working on a resubmission, which is due at the NIH on March 5th. In order to convincingly demonstrate the importance of CGD to the community, we ask that our users provide us with letters of support to accompany the application - please highlight how you use CGD, and how its discontinued availability would impact your research. We also ask you to take a few minutes and fill out a survey that will help us to identify specific needs of the community and highlight the role of CGD as a community resource. Please, follow the link here. We will greatly appreciate if you can email letters of support and complete the survey by February 15. Strong, unequivocal support is essential for continuing existence of CGD. (Posted January 22, 2014)

Assembly 22 of the C. albicans genome sequence

We are pleased to announce that Assembly 22 of the C. albicans SC5314 genome sequence has now become available at CGD, fully integrated into the CGD environment. Assembly 22 (A22) is described in Muzzey D., et al. (2013) Assembly of a phased, diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure. Genome Biol. 2013 Sep 11;14(9):R97.

Taking advantage of next-generation sequencing and achieving nearly 700-fold coverage, this phased, diploid assembly permits more sensitive, allele-specific analysis of the genome structure and funcion. A22 supersedes the previous Assembly 21 as the default genome sequence for C. albicans SC5314. All the previous assemblies remain available at CGD's download pages. (Posted June 27, 2014)

Introducing GeneXplorer for CGD

We have implemented GeneXplorer, a web tool for browsing and analysis of expression datasets and, so far, we have added microarray datasets from over 30 publications already archived at CGD. Each of those publication is linked via an icon to a GeneXplorer-generated web page that shows a colorimetric image of the clustered expression profiles. These images are zoomable and clickable (click on any profile to see the expression patterns of the most similarly or dissimilarly expressed genes). The publications are also linked (via ) to a downloadable data file in the pcl format. We are focusing our efforts on the microarray datasets and more publications are added to GeneXplorer every week. (Posted March 11, 2014)

2013 CGD News Archive

 

Peptide Atlas Links

The Protein Information tab for each Candida albicans gene now links to experimental mass spectrometry data at the Peptide Atlas web site. For example, the TUP1 Protein tab at CGD now features a section called "Experimental Observations" that links to the TUP1 Peptide Atlas Page, which shows the sequence and properties of experimentally observed peptides, as well as graphical displays of where these peptides align to the full-length protein. CGD thanks Concha Gil and Vital Vialas for contacting us with this suggestion. (Posted December 4, 2013)

Sequence trace files available

We have added archival Candida sequence data from the NCBI TraceDB site, and these data are now available from our download site. (Posted November 12, 2013)

ASM Candida Conference: abstract submission deadline approaching (25 November 2013)

You are cordially invited to the 12th ASM Conference on Candida and candidiasis, which will be held at the Hyatt Regency New Orleans, Louisiana, USA, on March 26-30, 2014. This promises to be an exciting meeting in a great location! Most talks at the conference will be selected from the submitted abstracts. The organizers invite abstracts on all aspects of Candida pathobiology genomics, molecular and cell biology, including host-fungus interactions, infection and antifungal therapy. We also encourage medical mycologists to submit abstracts on Candida Case Reports for a new session on this specific topic. The abstract submission deadline is 25 November.

ASM Candida12 website: http://conferences.asm.org/index.php/upcoming-conferences/12th-asm-conference-on-candida-and-candidiasis (Posted November 1, 2013)

Aspergillus nidulans and Neurospora crassa Orthologs

CGD Locus Summary pages now feature links to Aspergillus nidulans and Neurospora crassa orthologs alongside the links to Schizosaccharomyces pombe and Saccharomyces cerevisiae orthologs in the "Ortholog(s) in non-CGD species" section of the page (see example). The new A. nidulans links lead to the ortholog's Locus Summary page at the Aspergillus Genome Database and the N. crassa links lead to the gene pages at the Broad Institute. In addition, these new ortholog mappings are used for Gene Ontology annotation prediction in CGD. (Posted August 13, 2013)

Public Distribution of the Merck Candida albicans Double Barcoded (DBC) strain library

The National Reserarch Council of Canada has been mandated by Merck Sharp & Dohme Corp. for the distribution of its library of double barcoded Candida albicans mutants carrying heterozygous deletions. See Candida Community News for details. (Posted July 18, 2013)

Date for your diary - 12th ASM Conference on Candida and candidiasis

The 12th ASM Conference on Candida and candidiasis will be held in the Hyatt Regency New Orleans, Louisiana, USA, on March 26-30, 2014. The program includes sessions on Candida pathobiology, host-fungus interactions, infection and antifungal therapy. All sessions will be chaired by pre-eminent scientists in the field. As usual, most talks will be selected from the submitted abstracts. The organisers also encourage the submission of abstracts from medical mycologists for a new session on Candida Case Reports. This promises to be an exciting meeting in a great location!

Visit ASM Candida12 website: http://conferences.asm.org/index.php/upcoming-conferences/12th-asm-conference-on-candida-and-candidiasis
(Posted May 24, 2013)


C. dubliniensis Data in CGD

We are pleased to announce that CGD is now hosting the C. dubliniensis CD36 genome sequence and reference annotation. These data were formerly collected and maintained by the Sanger Institute's GeneDB resource. Special thanks to Derek Sullivan, Gary Moran, Martin Aslett, and Matthew Berriman for making it possible for CGD to provide these data to the research community when the GeneDB resource for C. dubliniensis went offline.

We provide Locus Summary pages for each C. dubliniensis gene, for example, Cd36_01180, BLAST, the GBrowse Genome Browser, Sequence Tools, and the full suite of downloadable files, including sequence, GFF, and protein domain files. (Posted April 30, 2013)

New features for C. dubliniensis, now included in CGD:
  • Addition of orthologs, and links among between Locus Summary pages for these orthologs within CGD
  • Ortholog and protein-domain-based Gene Ontology (GO) term predictions
  • Ortholog and protein-domain-based gene descriptions, for display on the Locus Summary pages
  • tRNA-Scan analysis
  • Curation of the experimental literature about C. dubliniensis, which will be an ongoing project at CGD going forward

We look forward to your feedback on these new data and features. (Posted June 6, 2013)

Additions and Improvements to Datasets Available for Download at CGD

CGD has added protein domain predictions for eight additional Candida strains:
  • C. albicans WO-1
  • C. dubliniensis CD36
  • C. guilliermondii ATCC 6260
  • C. lusitaniae ATCC 42720
  • C. orthopsilosis Co 90-125
  • C. tropicalis MYA-3404
  • D. hansenii CBS767
  • L. elongisporus NRLL YB-4239
Domain predictions were made using InterProScan software from the European Bioinformatics Institute (EBI). They are available on our Domain Download pages. Domain predictions for the three Candida strains actively curated by CGD are also available.

We now provide stable links to the current downloads of CGD sequence files, GFF files and chromosomal features files. These links have the same names as the primary download files, except that the frequently-changing genome version identifier in the name is replaced with the constant term "current". Thus, when the names of the primary files change because of an update in the genome version, the names of the links will stay the same, facilitating automated access to the data.

We have also made general updates to the informative text on the download pages. We hope you will find these additions and improvements useful. (Posted January 24, 2013)

2012 CGD News Archive

 

CGD Infrastructure Improvements

We are pleased to announce that the main CGD servers are back online, now housed in a new data facility that provides a faster network and more stable environment than the previous location. The CGD Pathways and Full-Text Literature Search tools will be back in service soon. All other tools and resources are fully functional. We thank you for your patience and support during the outage. (Posted December 4, 2012)

Non-redundant library containing a total of 2,357 different Candida albicans mutants available

The National Reserarch Council of Canada starts distributing a Candida albicans GRACE (gene replacement and conditional expression) library. See Candida Community News for details. (Posted November 6, 2012)

Auto-suggest Feature in the CGD Quick Search

We have added a new real-time suggestion feature to our Quick Search. As you type a query into the box, likely search terms from the database are now displayed in a pull-down menu below. We hope that this makes it easier for you to find the information you need, and we welcome your comments or suggestions. (Posted August 1, 2012)

CGD Orthologs Now Derived from CGOB

We are pleased to announce that we are now using the curated synteny information provided by the Candida Gene Order Browser (CGOB) for CGD's ortholog mappings among Candida species, and between Candida species and S. cerevisiae. This information is used to link the Locus Summary Pages of orthologous genes between CGD species (under the section "Orthologous genes in Candida species"; see this example). The ortholog mappings between each pair of species are also available in our download pages. We thank Sarah Maguire and Geraldine Butler of the Conway Institute, University College Dublin, for making the CGOB data available to CGD. (Posted July 12, 2012)

Candida orthopsilosis Sequence and BLAST Datasets now available at CGD

The sequence of C. orthopsilosis strain Co 90-125, described in Riccombeni et al. (2012), has been added to the the CGD sequence downloads and BLAST datasets. The sequence and annotation was obtained by CGD from EBI. (Posted June 11, 2012)

CGD Genome Browser Upgrade

We now feature a new and improved version of the Genome Browser in CGD. For example, view a region of C. albicans Chromosome 1. In GBrowse2, the order of the data tracks in the display can be easily rearranged by drag-and-drop. In addition, the interface can smoothly switch among species, and between genomic and protein views, using the selections in the Data Source pull-down menu. The new interface provides tabs with track selection and various customization options. GBrowse is developed by the Generic Model Organism Database GMOD project. We look forward to your feedback. (Posted May 23, 2012)

New look for CGD website

We are pleased to announce that CGD has been upgraded to a more streamlined look, with a new home page and improved navigation options. It may be necessary to clear cached pages and restart your web browser for the new pages to render properly. CGD thanks the Berman, Johnson, and Brand labs for the beautiful color images, now displayed on the CGD home page. CGD welcomes your feedback. (Posted May 8, 2012)

Intergenic Sequence Downloads

CGD provides two new methods for obtaining intergenic sequences. (1) From the locus summary page of any feature (click here for an example), click on the pull-down menu under "Retrieve Sequences" on the right side of the page, select "DNA plus flanking intergenic seq for...", and then click "View". (2) From the sequence download page for an organism in CGD (click here for an example); the relevant download files end with "_orf_plus_intergenic.fasta.gz", which contain protein-coding genes plus intergenic regions or "_other_features_plus_intergenic.fasta.gz", which contain other genes (for example, non-coding RNAs) plus intergenic regions. In all cases, we provide the sequence of the feature itself plus sequence extending upstream and downstream to the boundary of the next transcribed feature (exclusive). For protein-coding genes that boundary is the start or stop codon, for non-coding RNAs it is the 5' or 3' end of the mature RNA. (Posted April 24, 2012)

Improved Web Performance at CGD

We are pleased to announce that the CGD website has a new server. We are excited about the new speed and responsiveness of the CGD web pages as a result of our migration to a new Linux system. Our benchmark testing indicates that the new system processes web pages and tools, such as BLAST, approximately 3 times faster than our old server. We thank you for your patience during the down-time on Tuesday March 20, 2012, which was necessary to switch the database over to the new server. We hope you will enjoy the improved performance of the CGD website. (Posted March 22, 2012)

C. parapsilosis Data in CGD

We are pleased to announce that we have now added C. parapsilosis information into CGD. C. parapsilosis is the third Candida species for which manually curated data are available in our database. This latest C. parapsilosis reference sequence and annotation includes the extensive set of refinements published by Geraldine Butler and colleagues in Guida et al. (2011). The data loading is complete, and:
  • C. parapsilosis CDC317 sequence is now available in all of the CGD tools
  • Each C. parapsilosis gene now has a Locus Summary page in the database
  • C. parapsilosis genome and annotation is available in the GBrowse Genome Browser
  • We have used tRNA-Scan to refine and update the C. parapsilosis tRNA predictions; like the protein-coding genes, the tRNA genes each have a Locus Summary page in the database
  • Genes have been assigned predicted function, process, and localization annotations (Gene Ontology terms) based on orthology to S. cerevisiae, S. pombe, C. albicans, and C. glabrata
  • Additionally, protein-coding genes have been assigned predicted annotations based on protein motifs and domains (InterPro)
  • Manual curation of the published scientific literature about C. parapsilosis genes is ongoing, and experimental data collected from the literature will continue to be added
We look forward to your feedback on the new C. parapsilosis species data in CGD. (Posted March 15, 2012)

2011 CGD News Archive

 

Updated tRNA Annotation

We have updated the annotation of C. albicans and C. glabrata tRNA genes, based on predictions using tRNAscan-SE and comparisons with S. cerevisiae homologs. Changes include modification of intron boundaries for all intron-containing tRNAs of C. glabrata, and annotation strand changes to several C. albicans mitochondrial tRNAs. In addition, tRNA names and aliases have been updated, as outlined in the CGD Nomenclature Guide. (Posted July 25, 2011)

11th ASM Conference on Candida and Candidiasis

The 11th ASM Conference on Candida and Candidiasis will take place from March 29 to April 2, 2012 at the San Francisco Hyatt. Registration and abstract submission will open in Fall 2011. Please see the meeting web site for details. (Posted July 25, 2011)

New Additions to Highlights in Candida Biology

CGD curators have compiled a set of references on a variety of topics relevant to Candida biology. We have recently added new bibliographies and topic areas for C. glabrata. The reference lists are intended to provide a brief overview of each subject area, including many key reviews, and to serve as a resource for those new to research in Candida biology. (Posted July 19, 2011)

Seeking Community Input

We have completed our curatorial review of the scientific literature about genes from C. albicans and C. glabrata, and would welcome you to review the information posted for the genes with which you are familiar. If there in any information that is inaccurate or incomplete, or if we are missing any references that should be cited, please let us know. We greatly appreciate your help in improving this community resource! (Posted July 18, 2011)

CGD is on Facebook

CGD now has its own page on Facebook, where we will post occasional updates and announcements.
To see the CGD posts in your Facebook news feed, you may "like" the page. (Posted July 8, 2011)

Introducing Multispecies CGD, with C. glabrata and C. albicans Curation

We are pleased to announce that we have now fully integrated C. glabrata information into CGD. We have curated the entire published experimental literature that describes C. glabrata genes, as well as the C. albicans literature, and have made extensive updates to the CGD database and software to store and query information across multiple species simultaneously.
    New and updated functionalities include:

  • Each C. glabrata CBS138 gene has its own Locus Summary page in CGD; see, for example, the C. glabrata CDR1/CAGL0M01760g Locus Summary page.

  • The CGD Locus Summary pages for each gene, in C. glabrata as well as C. albicans, contain a newly expanded section describing orthology within the Candida, as well as orthologs in S. cerevisiae. Hyperlinks connect the CGD Locus Summary pages between orthologous C. albicans and C. glabrata genes.

  • We have curated the entire published experimental literature that describes C. glabrata genes, and have written gene descriptions, compiled citation lists, assigned Gene Ontology (GO) terms, and collected mutant phenotypes for every characterized gene. We have also leveraged orthology with C. albicans and S. cerevisiae to make predictions about the function, role, and localization of C. glabrata genes that have characterized orthologs in these other species. All of this information is fully available on the CGD web site and in the CGD downloadable files.

  • The sequence of the C. glabrata CBS138 genome is available in the CGD searches.

  • We have implemented a multispecies BLAST tool, in which any subset of the multiple Candida genomes can be selected and searched simultaneously.

  • The CGD Search tools, including the Quick Search, BLAST, Gene/Sequence search, Ortholog Search, and the Pattern Matching Tool, have all been updated to query multiple species.

  • Quick Search results are now displayed in sections organized by species. Results that are not species-specific (e.g., individual GO terms, colleagues, references) are listed in a separate section on the results page.

  • The Protein Information page (Protein tab) has been updated and reorganized to consolidate the information and links from the Protein Info, Domains/Motifs and Physiochemical Properties subtabs onto a single, more browseable page.

  • Genome Snapshots are provided for both C. albicans and for C. glabrata, summarizing the status of the genome annotation on a daily basis.

We welcome your feedback on how we can improve the CGD site and interface to make it more useful for your research. Please contact us any time. (Posted June, 2011)

Protein-domain-based Gene Ontology (GO) term predictions in CGD

We have now added predictions about gene product function, role, and localization based on protein domains and motifs. Protein domains were determined using the InterProScan software from the European Bioinformatics Institute (EBI), and then domain-based Gene Ontology (GO) term assignments are made using the InterPro-to-GO mappings from GO Consortium web site. (Posted June, 2011)

Links to PhylomeDB phylogenetic gene trees

We have added links from CGD to phylogenetic gene tree pages in PhylomeDB. PhylomeDB is a public database of gene phylogenies (phylomes), for exploration of the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. You may access the phylogenetic tree (for example, this tree for the gene encoding actin) from the new "PhylomeDB" link in the External Links section of each gene's Locus Summary page in CGD, located below the Sequence Information section on the page. (Posted April 5, 2011)

2010 CGD News Archive

 

Description lines for uncharacterized gene products, based on S. cerevisiae orthologs and predicted Gene Ontology (GO) annotations

For genes that lack experimental characterization, but which have characterized orthologs in S. cerevisiae, we have now added Description lines to the CGD Locus Summary pages to note the orthology relationships and, where possible, predictions about gene function or localization. The procedures and criteria used to make these predictions are described in more detail here. (Posted November 19, 2010)

Sellam et al. (2010) data added to CGD

A set of new data from a genome-wide experimental annotation study by Sellam et al. (2010) has been added to CGD. Displayed as a GBrowse track are 2,172 previously unknown transcribed regions (see example), with genome-wide occupancy data for RNA polymerases I, II and III shown in the mouse-over window. Also, 49 predicted snoRNA genes are now included in the database. All datafiles are available at the download directory. Note: if the new track is not initially visible in your browser, refresh the GBrowse display by pressing Reset, which is the bright pink button located in the grey "Instructions" banner near the top of the page. (Posted October 12, 2010)

Pattern Matching within Intergenic Regions

The CGD Pattern Match tool now supports queries of the potential regulatory regions located between annotated features, in addition to the other chromosome- and feature-based sequence sets provided. To utilize this new feature, select "Intergenic regions" from the Sequence Database menu on the tool interface. You can search for specific sequence matches or for sequence patterns, using the character codes listed on the PatMatch tool page. (Posted September 1, 2010)

New Candida albicans Strains page at CGD

We have added a "Candida albicans Strains" page to CGD, with brief descriptions and references for some of the more commonly used laboratory strains, as well as a lineage diagram. If you would like to suggest additions, corrections, or updates to this list, please send a message to CGD curators with details. (Posted July 21, 2010)

Highlights in Candida Biology

A new bibliography resource is now available at CGD. Curators have compiled a set of references on a variety of topics relevant to Candida biology. The reference lists are intended to provide a brief overview of each subject area, including many key reviews, and to serve as a resource for those new to research in Candida biology. (Posted July 15, 2010)

Sequences for Additional Candida-related Species and Strains Now Available

CGD now provides for download sequences from several Candida and Candida-related species and strains in addition to C. albicans SC5314. The new additions include:
  • Candida albicans WO-1
  • Candida dubliniensis CD36
  • Candida glabrata CBS138
  • Candida guilliermondii ATCC 6260
  • Candida lusitaniae ATCC 42720
  • Candida parapsilosis CDC 317
  • Candida tropicalis MYA-3404
  • Debaryomyces hansenii CBS767
  • Lodderomyces elongisporus NRLL YB-4239
All sequences are available on the Sequence Downloads Page. See the Sequence Help Page for additional information. We will add additional strains and species as their genomic sequences become available. (Posted July 8, 2010)

New search options on Locus Summary pages

We have added two new search options to the "Literature" pull-down menu on each Locus Summary page (located directly below the GBrowse links on the right-hand sidebar). The "Full-text lit. search, gene name(s)" and "Full-text lit. search, gene name(s) and aliases" options link to the Textpresso tool, which supports searches of the full text of Candida albicans papers in CGD. The "gene name(s)" search pre-fills the keyword search box with the standard and systematic name of the gene, whereas the "gene name(s) and aliases" search also includes all of the gene synonyms or aliases listed in CGD. (Posted April 22, 2010)

Links to Candida Gene Order Browser

CGD now links to the Candida Gene Order Browser (CGOB), which is an online tool for visualizing the syntenic context of genes from multiple Candida genomes. A link to the synteny view for each C. albicans gene appears in the "External Links" section of the CGD Locus Summary Page. CGOB is developed by David Fitzpatrick and Geraldine Butler at the University College Dublin, Ireland. (Posted April 13, 2010)

Updated comparisons to S. cerevisiae

Ortholog and Best Hit mappings of C. albicans genes to S. cerevisiae genes have been updated based on the latest Assembly 21 sequence of the C. albicans genome and the latest annotation at the Saccharomyces Genome Database (SGD). These appear as hyperlinks between CGD Locus Pages and the corresponding Locus Pages at SGD. S. cerevisiae best hits and orthologs are searchable using the Quick Search or the S. cerevisiae Orthologs and Best Hits Search tool on the CGD Full Search page, and a file containing all of the ortholog and Best Hit mappings may be downloaded from the homolog directory on the CGD Downloads site. Gene Ontology (GO) annotations have also been updated at CGD based on the updated S. cerevisiae ortholog mappings and the latest GO information at SGD. The procedure used for the transfer of GO annotations is described in further detail here. Based on orthology, we have inferred 13,424 GO annotations for 3,324 C. albicans genes in CGD. (Posted March 30, 2009)

CGD now contains comprehensive Gene Ontology annotations for C. albicans gene products

CGD curators have reviewed all of the gene-specific literature for C. albicans and are curating the new literature on an ongoing basis. Because all of the available literature has been considered, we have now assigned Gene Ontology (GO) annotations to the root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" to gene products for which there are no experimental or computational data that would allow annotation with a non-unknown GO term. The evidence code for these "unknown" annotations, ND (No biological Data available), indicates that curators have searched for but have not found any relevant information as of the annotation date. CGD is now "GO complete", meaning that each gene product has a GO annotation (including unknowns) in each of the three GO aspects. (Posted March 11, 2010)

Expanded phenotype data and new curation system in CGD

CGD is now releasing our improved and expanded mutant phenotype pages. We have implemented a controlled-vocabulary system for phenotype curation that is already in use by AspGD and SGD. This system greatly increases the amount of detailed information that can be captured for each phenotype, and facilitates searching and comparison of mutant phenotypes. Each phenotype annotation contains a term representing the entity or process that is observed (e.g., hyphal growth, carbon source utilization, virulence; view the complete list) and a qualifier that describes the effect on that entity or process in the mutant (e.g., decreased, increased, abnormal). Additional fields display information such as strain background, allele name, conditions under which the phenotype is observed, or the identity of relevant chemicals. A brief version of the phenotype is displayed on the Locus Summary page for each gene, and the complete information is accessible via the 'Phenotype' tab at the top of the page. All of the information is searchable via CGD's Quick Search and Expanded Phenotype Search, and may also be downloaded in bulk using CGD's Batch Download tool or Download Data page. (Posted February 24, 2010)

CGD Protein Information Pages now available

CGD has expanded to include protein information for all verified and predicted ORFs. Using software and database tools developed at the Saccharomyces Genome Database (SGD), the Protein Information Pages display basic property, domain organization, structural and homology information. To view the page for a given protein, navigate to the Locus Summary page for the corresponding gene and click on the "Protein" tab towards the top of the page. Example Protein Pages: Act1p; Cdc28p; Orf19.4531p. (Posted February 5, 2010)

CGD hosts phenotype images and viewer from Homann et al. study

A collection of 100,000 images representing the mutant phenotypes reported in Homann et al. (2009) A phenotypic profile of the Candida albicans regulatory network. PLoS Genet 5(12):e1000783 is now available at CGD, along with a Java application that allows searching and viewing of the images. In this study, the phenotypes of 143 homozygous null mutant strains, each deleted for a known or putative transcription factor gene, were assayed under multiple conditions. To access these images, download and install the Phenotype Viewer software (available in both PC/Linux and Mac versions). We thank Oliver Homann for providing the data and application and for help in incorporating the data into CGD. (posted January 13, 2010)

2009 CGD News Archive

 

Registration now open for the 10th ASM Conference on Candida and Candidiasis

The 10th ASM Conference on Candida and Candidiasis will take place from March 22-26, 2010, at the Hyatt Regency in Miami, Florida. Registration and abstract submissions are now open, at the meeting web site. Abstracts are due by January 15, 2010. (Posted December 17, 2009)

Updated comparisons to S. cerevisiae

Ortholog and Best Hit mappings of C. albicans genes to S. cerevisiae genes have been updated based on the latest Assembly 21 sequence of the C. albicans genome and the latest annotation at the Saccharomyces Genome Database (SGD). These appear as hyperlinks between CGD Locus Pages and the corresponding Locus Pages at SGD. S. cerevisiae best hits and orthologs are searchable using the Quick Search or the S. cerevisiae Orthologs and Best Hits Search tool on the CGD Full Search page, and a file containing all of the ortholog and Best Hit mappings may be downloaded from the homolog directory on the CGD Downloads site. Gene Ontology (GO) annotations have also been updated at CGD based on the updated S. cerevisiae ortholog mappings and the latest GO information at SGD. The procedure used for the transfer of GO annotations is described in further detail here. Based on orthology, we have inferred 13202 GO annotations for 3314 C. albicans genes in CGD. (Posted December 3, 2009)

CGD paper in Nucleic Acids Research Database Issue

A paper entitled "New tools at the Candida Genome Database: biochemical pathways and full-text literature search" will appear in the 2010 Database Issue of Nucleic Acids Research. The paper is now available online as a Nucleic Acids Research Advance Access article. (Posted October 7, 2009)

Three new resources for the Candida community

Carol Munro, University of Aberdeen, and Christophe d'Enfert, Institut Pasteur, have recently received funding from the Wellcome Trust, UK to create three new resources for the Candida community. The three main goals of the project will be to create (1) a C. albicans ORFeome library by cloning every predicted ORF into a Gateway® vector in E. coli, (2) a library of bar-coded C. albicans over-expression vectors by placing each ORF under the control of a reverse Tetracycline promoter in a C. albicans integrative plasmid based on CIp10 and (3) a library of C. albicans strains each over-expressing a single gene by integrating the plasmids generated in (2) into the RPS1 chromosomal locus. Each ORF will be verified by sequencing both ends. The funding ends in September 2012 and at this point the 3 collections will be made available to the community and distributed for a small fee that will cover maintenance and distribution costs. Contact Carol Munro (c.a.munro@abdn.ac.uk) or Christophe d'Enfert (christophe.denfert@pasteur.fr) for more information. (Posted September 29, 2009)

10th ASM Conference on Candida and Candidiasis

The 10th ASM Conference on Candida and Candidiasis will take place from March 22-26, 2010, at the Hyatt Regency in Miami Florida. Abstract submissions will open in Fall 2009. Please see the meeting web site for details. (Posted May 10, 2009)

Search full text of Candida journal articles with Textpresso

A full-text literature search capability has now been added to CGD. The literature search tool is powered by Textpresso, a text-mining tool developed at Wormbase (Muller H, et al. (2004) PLoS Biol. 2(11):e309). Currently, the application contains over 16,500 Candida-related full-text journal articles. The full-text literature search can be accessed via the Full-text Search link on the sidebar on the CGD home page, and is also available as a link on the Search Options contents page. (Posted April 14, 2009)

CGD grant renewal

We are very pleased to announce that the National Institute of Dental & Craniofacial Research at the US National Institutes of Health has renewed the grant that funds CGD. We thank the many members of the scientific community who made this possible by writing letters of support. We look forward to another five years of service to the Candida research community. (Posted April 2, 2009)

Updated comparisons to S. cerevisiae

Ortholog and Best Hit mappings of C. albicans genes to S. cerevisiae genes have been updated based on the latest Assembly 21 sequence of the C. albicans genome and the latest annotation at the Saccharomyces Genome Database (SGD). These appear as hyperlinks between CGD Locus Pages and the corresponding Locus Pages at SGD. S. cerevisiae best hits and orthologs are searchable using the Quick Search or the S. cerevisiae Orthologs and Best Hits Search tool on the CGD Full Search page, and a file containing all of the ortholog and Best Hit mappings may be downloaded from the homolog directory on the CGD Downloads site. Gene Ontology (GO) annotations have also been updated at CGD based on the updated S. cerevisiae ortholog mappings and the latest GO information at SGD. The procedure used for the transfer of GO annotations is described in further detail here. Based on orthology, we have inferred 12502 GO annotations for 3282 unique features in CGD. (Posted March 26, 2009)

New gene name aliases in CGD

In order to improve the traceability of historical names for C. albicans genes, we have incorporated additional alias names into CGD. Locus tags that were assigned in the GenBank entries for the original Assembly 19 genomic sequence from the Stanford Genome Technology Center have been added to CGD Locus Summary pages for open reading frames. These locus tags are in the format "CaO19.1234", where the numerals after the period identify the open reading frame and are the same as those used in the systematic names such as "orf19.1234". We have also added large sets of identifiers from CandidaDB and Entrez gene. Thanks to Christophe d'Enfert for providing us with the CandidaDB alias names and their mappings. (Posted February 20, 2009)

More convenient sequence download options at CGD

We have made enhancements to two tools, Gene/Sequence Resources and Batch Download, that increase their flexibility for downloading the sequences of multiple genomic regions. Gene/Sequence Resources now accepts as input a file containing the coordinates of multiple chromosomal or contig regions in order to generate a file containing those sequences. Batch Download, which retrieves sequence and other information for annotated genes and other features within a specified region, now allows you to specify a custom length of upstream and downstream flanking sequence to be included with the sequence of each feature. For more details on these tools, please click the "Help" button in the upper right-hand section of each of the interfaces. (Posted January 27, 2009)

2008 CGD News Archive

 

New Genome Snapshot resource

We have created a resource, Genome Snapshot, that provides a daily count of C. albicans genomic features and a summary of Gene Ontology (GO) annotations. This page displays a pie chart showing the number of Verified, Uncharacterized, and Dubious protein coding genes; an inventory of all the genomic features by chromosome; a summary of GO annotations; and the distribution of GO annotations for C. albicans gene products in the Process, Function and Component Ontologies. There is a link to the Genome Snapshot page on CGD's Home page under "CGD Curation News", and there are also links in the "About CGD" section of the left-hand sidebar that appears on CGD's home page and other index pages, and on the About CGD page. (Posted December 3, 2008)

Updated comparisons to S. cerevisiae

Ortholog and Best Hit mappings of C. albicans genes to S. cerevisiae genes were updated based on the latest Assembly 21 sequence of the C. albicans genome. These Orthologs and Best Hits appear as hyperlinks between CGD Locus Pages and the corresponding Locus Pages at the Saccharomyces Genome Database (SGD). S. cerevisiae Best Hits and orthologs are searchable using the Quick Search or the S. cerevisiae Orthologs and Best Hits Search tool on the CGD Full Search page, and a file containing all of the ortholog and Best Hit mappings may be downloaded from the homolog directory on the CGD Downloads site.

Gene Ontology (GO) annotations have also been updated at CGD based on the updated annotations of S. cerevisiae orthologs at SGD. The procedure used for the transfer of GO annotations is described in further detail here. (Posted November 14, 2008)

CGD usage: Two million hits

The CGD web site has been accessed over 2,000,000 times, and as we celebrate this milestone, CGD would like to thank the Candida research community for your continued support. (Posted November 11, 2008)

Multiple updates to Assembly 21 sequence and annotation

In collaboration with Mike Lin, Christina Cuomo, Manolis Kellis, and their colleagues at the Broad Institute, we have employed 100 Mb of new sequence data for C. albicans strain SC5314 and a comparative genomic analysis of 8 closely related species to make hundreds of updates to the Assembly 21 reference sequence (Butler et al., in preparation; see the CGD Sequence Documentation). New genes have been added to the gene catalog; all artificial "adjustments" to the sequence have been examined and corrected; and the boundaries of coding sequences and introns have been updated. 181 ORFs have been classified as "Dubious" because they are indistinguishable from random sequence; the remaining ORFs have been assigned "Verified" or "Uncharacterized" classifications to indicate whether or not there is experimental evidence for the existence of a gene product.

Updates for each chromosome are enumerated in a Summary Table, which is linked to Chromosome History pages that provide a detailed list of all the updates for each chromosome. The Locus History page for each chromosomal feature that was examined contains a note that describes the changes that were made to that feature. In all, 73 new ORFs and 8 new pseudogenes have been added, the coordinates of 63 ORFs have been updated, and 697 sequence updates have been made. (Posted November 7, 2008)


Additional formats available for sequence retrieval

Two additional sequence formats (Decorated FASTA and Numbered Sequence) are now available via the Gene/Seq Resource tool, and the sequence retrieval pull-down options from Locus Summary pages. Decorated FASTA format, provided for genomic DNA sequence of all CGD features, displays color-coding for different parts of a selected region, such as coding sequence vs. flanking sequence. The Numbered sequence format, provided for the Exon(s) only sequence of coding features, formats the sequence as codons and numbers it beginning at the start codon. For further details, please refer to the Gene/Seq Resources help page. (Posted October 10, 2008)

CGD Pathways server upgrade

Candida Biochemical Pathways at CGD have been moved to a new, faster server at http://pathway.candidagenome.org/. Please update any bookmarks or locally stored links to Pathway pages, as the old URL will be discontinued. (Posted October 7, 2008)

Assembly 20 moving to archival storage

We have removed access to Assembly 20 sequences from the Locus Summary pages, as well as from GBrowse, and from most sequence analysis tools. Assembly 20 datasets will remain available for BLAST searches, and the Assembly 20-based sequence datasets will continue to be available for download from the CGD web site, but these archival files will not be regularly updated. (Posted October 7, 2008)

Links to RefSeq Nucleotide and Entrez Gene records now available

Candida genes have been computationally mapped to RefSeq Nucleotide sequences and Entrez Gene records based on exact sequence similarity. Links to the appropriate RefSeq and Entrez Gene records are available in the "External Links" section of CGD Locus Summary pages (Examples: orf19.6115, HWP1). The data are also available for download from our website. (Posted October 7, 2008)

Batch search for S. cerevisiae orthologs and best hits now available

S. cerevisiae orthologs and best hits can now be searched for multiple C. albicans genes using the Batch Download Tool. The results of the batch ortholog and best hit search will be provided as a tab-delimited file containing the corresponding S. cerevisiae gene name and SGDID, along with an indication of whether the S. cerevisiae gene is an ortholog or best hit. Please refer to the help document here for further details. (Posted May 8, 2008)

Links to C. dubliniensis orthologs now available

Orthologs between C. albicans and C. dubliniensis are now available on the "Ortholog(s)" section at CGD Locus pages and hyperlinked to appropriate GeneDB pages (Examples: ECM331, MKC1). The data are also available for download from our web site. The ortholog mappings between C. albicans and C. dubliniensis were provided to CGD by John Gamble and Matthew Berriman at the Wellcome Trust Sanger Institute. The C. dubliniensis orthologs are manually curated positional orthologs based on synteny. (Posted May 1, 2008)

Updated comparisons to S. cerevisiae

We have updated CGD's comparisons between C. albicans and S. cerevisiae protein-coding genes in two different areas.

Ortholog and Best Hit mappings of C. albicans genes to S. cerevisiae genes were updated based on Assembly 21 of the C. albicans genome. These Orthologs and Best Hits appear as hyperlinks between CGD Locus Pages and the corresponding Locus Pages at the Saccharomyces Genome Database (SGD). S. cerevisiae Best Hits and orthologs are searchable using the Quick Search or the S. cerevisiae Orthologs and Best Hits Search tool on the CGD Full Search page, and a file containing all of the ortholog and Best Hit mappings may be downloaded from the S. cerevisiae orthologs and Best Hits directory on the CGD Downloads site.

New Gene Ontology (GO) annotations have been added to CGD based on the annotations of S. cerevisiae orthologs at SGD. Annotations in SGD based on direct experimentation (evidence codes IDA, IPI, IGI, and IMP) were assigned to the orthologous C. albicans gene products. The CGD annotations predicted by this method have the IEA (Inferred from Electronic Annotation) evidence code and are indicated as computationally assigned. Annotations that were redundant with existing CGD manually curated GO terms or with other newly predicted annotations were removed from the set. In total, 11191 new annotations were added to 3113 genes. The procedure used for the transfer of GO annotations is described in further detail here. (Posted April 23, 2008)

New Files Available for Download

CGD metabolic pathway information is now available in a tab-delimited file containing pathway names and lists of the genes that encode enzymes that participate in each pathway. We have also posted a file that contains the entire set of CGD pathway information in the format that is read by the Pathway Tools software from SRI. Both files are available for download from our web site.

We have also generated a file of annotations of Candida albicans genes to CGD GO Slim terms. A GO Slim is a small subset of terms from the Gene Ontology that is intended to provide a general overview without all the fine-grained detail contained in the GO itself. The CGD Downloads site has a new browsable go/ subdirectory containing files related to the Gene Ontology, including the GO annotation (gene_association) file containing the annotation of Candida albicans genes to terms from the complete Gene Ontology (the most precise and comprehensive GO annotation file at CGD), the less fine-grained CGD GO Slim annotations file containing annotation of Candida albicans genes to GO Slim terms, and the set of CGD GO Slim terms themselves. (Posted April 11, 2008)

CGD User Survey

In order to better serve the needs of the Candida community, CGD would like to know how you use CGD and to solicit your opinions on future directions. We request that every CGD user fill out a brief survey, which may be taken anonymously, about your use of CGD and the directions in which it should develop. Please click here to take the survey online. CGD staff will also have paper copies of the survey to distribute at the 9th ASM Conference on Candida and Candidiasis, March 24-28. We look forward to meeting you there and to receiving your feedback about CGD. (Posted March 21, 2008)

New Links from CGD Locus Pages

CGD Locus pages are now hyperlinked to additional resources for Candida gene information. These hyperlinks have been added to the External Links section, which appears below the sequence information on each Locus page. The new links entitled "Broad" connect to the Candida comparative annotation site at the Broad Institute. New "UniProt/Swiss-Prot" links connect to the corresponding UniProtKB records. In addition, the "CandidaDB" links in CGD have now been now updated to connect to the multi-genome version of CandidaDB at the Institut Pasteur. CGD thanks Christina Cuomo, Dan Barrell, Kati Laiho, Christophe d'Enfert, and Tristan Rossignol for their help in establishing these links. (Posted April 4, 2008)

Candida Biochemical Pathways are now available at CGD

Graphical, interactive displays of Candida biochemical pathways are now available at CGD. To access the pathway displays, you may browse from a list of hyperlinked CGD pathways, search from the main Pathway Search page, or click on the links that appear on Locus Summary pages of genes involved in a pathway. The pathways were created using the Pathway Tools software, which is developed and maintained by the Bioinformatics Research Group at SRI International. The pathway predictions are being manually reviewed and curated at CGD, as described in more detail on our Pathways Help page. Pathway curation is an ongoing process, and we welcome your suggestions for new pathways, or any corrections to metabolic pathway information in CGD. (Posted March 13, 2008)

2007 CGD News Archive

 

New Features at CGD

We are very pleased to announce significant enhancements to our web site, which have been implemented in collaboration with the Saccharomyces Genome Database. Some highlights: We welcome your feedback! (posted December 4, 2007)

DSHB-Microbe: a monoclonal antibody resource for the microbial research community

The Developmental Studies Hybridoma Bank (DSHB) is a national resource established under the auspices of the National Institutes of Health to maintain and distribute at cost hybridomas and their monoclonal antibodies to the general scientific community. The DSHB has now embarked on a new mission, to generate a bank, the DSHB-Microbe (dshb.biology.uiowa.edu), that will maintain and distribute hybridomas and their antibodies against microbial antigens. DSHB-Microbe is now accepting hybridomas from microbial research laboratories. Please see the CGD Community News page for additional information. (Posted November 5, 2007)

New Release of CandidaDB

An updated version of CandidaDB (http://genodb.pasteur.fr/CandidaDB) has just been released by Christophe d'Enfert at the Institut Pasteur. CandidaDB now contains information from nine genomes, including C. albicans SC5314. The database provides pre-run comparative ORF analyses (bi-directional best hits, ClustalW, protein families), and analysis of PFAM domains and topological features. (Posted October 25, 2007)

Assembly 21 of the C. albicans genome sequence

We are pleased to announce that Assembly 21 of the C. albicans genome sequence is now fully integrated and available at CGD. Assembly 21 (A21) is described in van het Hoog M, et al. (2007) Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 8(4):R52. This assembly resolves the issues in Assembly 20 due to the incorporation of WO-1 genome sequence, and is based on the sequence reads from strain SC5314 from the Stanford Genome Technology Center. In addition to making a chromosomal level assembly, by mapping the contigs of Assembly 19 (A19) to chromosomes and filling many of the gaps between them, the authors also made other numerous and widespread modifications to the genomic sequence, which are detailed on the Sequence Documentation page.

The coordinates of each ORF in A21 were determined at CGD using a sequence-based mapping procedure. We have also conducted a series of analyses of the A21 ORF set, the results of which are available for download and described in detail here.

Some highlights:

  • Get Assembly 21 sequence from the "Retrieve Sequences" menu on each Locus page (view example Locus page).
  • Browse Assembly 21 using the GBrowse Genome Browser, and see where all features from the historic asemblies map to A21 chromosomes (view example).
  • Download Assembly 21 files: sequence files, and sequence alignments and analyses (see the Sequence Documentation page).
  • View Assembly 21 chromosomal coordinates on CGD Locus pages.
  • BLAST Assembly 21 sequences.
  • See the type of change, if any, that affected each ORF between Assembly 21 and Assembly 20 or Assembly 19 (Noted in the Locus History Notes section for each ORF).
  • View the Chromosomal Features Table (see features flanking ACT1, for example) via the "Maps and Displays" menu on each Locus page.
  • Search for gene or chromosome sequence from Assembly 21 using the CGD Sequence Retrieval tool.
  • Expanded content in the Locus/Feature History Notes section, linked off each Locus page (view example).
Assembly 21 contains 6109 predicted protein-coding genes, including 13 mitochondrial ORFs. A total of 352 genes contain introns within the coding region. Assembly 21 also contains 156 predicted tRNA-encoding genes, 30 of which are mitochondrial. 5319 ORFs remain unchanged between Assemblies 19, 20, and 21, and four ORFs were deleted between Assembly 20 and 21. Please see the Sequence Documentation page for more details. (Posted September 21, 2007)

Download directories restructured for easy navigation

The download site at CGD has been reorganized to provide easier and more intuitive access to various sequence and other downloadable files. All sequence files are grouped and placed in separate directories for each genome assemblies of C. albicans. All hyperlinks to any download files have been updated and reflect the new locations. (Posted September 21, 2007)

Links to Fungal Orthogroups Repository web site

CGD now contains links to the ortholog group pages at the Fungal Orthogroups Repository, described by Wapinski et al. (2007) in "Natural history and evolutionary principles of gene duplication in fungi." Nature, 449(7158):54-61. To view the orthogroup, select the link entitled "Fungal Orthologs," which is located on the list of "External Links" near the bottom of each CGD Locus page. (Posted September 6, 2007)

Candida albicans SNP data from Forche et al. available on CGD GBrowse

SNP data from Forche A, Magee PT, Magee BB, May G Genome-wide single-nucleotide polymorphism map for Candida albicans. Eukaryotic Cell. 2004 Jun;3(3):705-14 are now available at CGD. SNP locations were mapped to each C. albicans genome assembly using the original marker sequences, and SNPs can be viewed in the GBrowse Genome Browser by selecting the "SNP" track. An example can be viewed here. Please note that you may need to select the checkbox next to the SNP track, which is listed under "General tracks," and then select "Update Image" to see the SNPs. (Posted August 31, 2007)

Optical Mapping Data Available

Optical Mapping data from P.T. Magee for C. albicans strain SC5314, generated by OpGen, are now available (right-click, or Ctrl-click on the link, and save the linked file to your computer). These data can be viewed using the OpGen MapViewer; to compare the optical mapping data to Assembly 21, start the MapViewer, and load the data file by selecting the menu item "File->Open Alignment". For more information, see the README document. Special thanks to P.T. Magee for providing the optical mapping data. (Posted August 7th, 2007)

9th ASM Conference on Candida and Candidiasis

The 9th ASM Conference on Candida and Candidiasis will take place from March 24-28, 2008, just outside of New York City. Abstract submissions will open in Fall 2007. Student Travel Grants are available. Please see the meeting web site for details, including the preliminary meeting program. (Posted July 6, 2007)

Intron data from Mitrovich et al. in CGD

A systematic analysis of introns in the C. albicans genome has been published: Mitrovich QM, Tuch BB, Guthrie C, Johnson AD. Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res. 2007 Apr;17(4):492-502. The intron data are now available in CGD. Please note that this dataset now allows CGD to clearly separate the introns in Assembly 20 from the gaps that were introduced by the Annnotation Working Group (AWG) to compensate for presumed sequencing errors that interrupt ORFs. These gaps are now labeled "Adjustments" in Assembly 20 in CGD, and they should be considered markers for regions that require resequencing, rather than corrections to the assembly. Summary files listing introns and non-intron adjustments are available from the CGD Downloads site, and more detail is available on the CGD Sequence Documentation page. Special thanks to Quinn Mitrovich for providing data and advice. (Posted May 17, 2007)

Candida GO Slim added

A Candida-specific subset of Gene Ontology is now available for use with the GO Slim Term Mapper tool. The GO Slim is a set of broad, high-level GO terms that have been selected by CGD curators based on significance to Candida biology. The terms are displayed on the GO Slim Term Mapper page, and may also be downloaded in the goslim_candida.obo file. Please see CGD help for more information. (Posted May 7, 2007)

New Community Resource: Candida albicans microarrays

DNA oligonucleotide arrays representing the Candida albicans genome are available from the Genome Sequencing Center at Washington University. For more information, please see our CGD Community News page. (Posted May 2, 2007)

Assembly 21 Sequence Files

Candida albicans Assembly 21 (A21) sequence files have been submitted by the A21 collaborators and described in van Het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol. 2007 Apr 9;8(4):R52. The sequence files are available for download from the CGD Sequence Downloads directory. Please note that the sequences in these files are exactly as released to CGD by the A21 collaborators, and that they have not yet been subject to analyses at CGD. A21 will be made available on the CGD Locus pages after the sequence coordinates of each ORF in A21 have been determined, and after a suite of analyses has been performed on this new assembly. (Posted April 19, 2007)

S. cerevisiae Best Hits

To identify homologs at lower stringency than that required by the strict ortholog mapping criteria, and to supplement the S. cerevisiae ortholog mappings that appear on the CGD Locus pages, C. albcans genes that lack S. cerevisiae orthologs were subject to BLASTp comparison with an expectation value (E) of 1e-5 against the set of S. cerevisiae ORF translations from SGD. A total of 1010 S. cerevisiae Best Hits have been added to CGD Locus pages. These Best Hits appear as hyperlinks between CGD Locus Pages and the corresponding Locus Pages at the Saccharomyces Genome Database (SGD). S. cerevisiae Best Hits and orthologs are searchable using the Category Search tool on the CGD Full Search page, and a file containing all of the Best Hit mappings may be downloaded from the S. cerevisiae orthologs and Best Hits directory on the CGD Downloads site. (Posted April 12, 2007)

CGD paper published in Nucleic Acids Research Database Issue

A paper entitled "Sequence resources at the Candida Genome Database" has been published in the open-access online 2007 Database Issue of Nucleic Acids Research. (Posted January 9, 2007)

2006 CGD News Archive

 

View changes across genome assemblies in the Genome Browser

CGD has generated sequence-based mappings of the contigs from Assemblies 4, 5, 6, and 19 and the ORFs from Assemblies 6 and 19, onto the chromosomes from Assembly 20, and mappings of the older assembly information onto the Assembly 19 contigs. These "historic tracks" are available in the GBrowse Genome Browser, where they serve as a graphical representation of the evolution of the genome assembly.

The criteria used are described in detail in the README file associated with the downloadable summary mapping reports.

To clear cached settings that may interfere with the display of the historic tracks, click on the pink "Reset" button, which is located near the top of the page in the Genome Browser, directly above the "Reports and Analysis" pull-down menu.

Please note that the Assembly 19 ORFs are displayed in two tracks. The "Assem19 ORF (SGTC)" set is the original set of ORFs released by the Stanford Genome Technology Center (SGTC), as described in Jones et al. (2004) The Diploid Genome of Candida albicans. PNAS 101:7329-7334. The "Assem19 ORF (AWG)" set contains the ORFs after modification by the Annotation Working Group (AWG), as described in Braun et al. (2005) A human-curated annotation of the Candida albicans genome. PLoS Genet. 2005 Jul;1(1):36-57. There are differences between the two sets. For example, in this example view, orf19.12704 is present in the SGTC set and subsequently deleted by the AWG, whereas orf19.5236.1 was added de novo by the AWG. In this second example view, a complicated series of events is represented graphically. The orf6.7681 was present in Assembly 6, but subsequently removed by the SGTC in generation of Assembly 19. During review of Assembly 19, the AWG then reinstated an ORF in this position and named it orf19.5261.2. The AWG then deleted this reinstated ORF during generation of Assembly 20. (Posted December 12, 2006, updated April 12, 2007)

Recent additions to CGD

We have added a "hover" feature to the the detailed map in the GBrowse Genome Browser. Upon dragging the cursor over an ORF or Contig (see example), details about the feature are displayed, including its names and aliases, positional coordinates, and description. Special thanks to Mike Cherry for the code underlying this feature.

We have also loaded updated, Assembly 20-based mappings between C. albcans ORFs and their S. cerevisiae orthologs. The mappings were generated using the InParanoid software (version 1.35) developed at the Karolinska Institutet. The program was run on November 26, 2006, using BLAST version 2.2.15. The set of C. albicans proteins from CGD, based on Assembly 20, was compared to the latest set of S. cerevisiae proteins from the Candida Genome Database (CGD), and the latest set of C. elegans proteins from the Sanger Institute, wormpep 166, was used as an outgroup. Stringent cutoffs were set: BLOSUM80 (instead of the default BLOSUM62), and an InParanoid score of 100%. In total, 3600 pairs of ortholog mappings met these criteria; these orthologs have been loaded into CGD, where they appear as hyperlinks between CGD Locus Pages and the corresponding CGD Locus Pages. (Posted November 28, 2006)

WARNING: Assembly 20 Sequence Advisory

The collaborative group who generated Assembly 20 has discovered that the sequence traces that they had been using to fill some of the gaps and determine overlaps between Assembly 19 contigs were derived from strain WO-1, rather than from the reference strain, SC5314. The sequence of these regions therefore is likely to be inaccurate with respect to the sequence of the reference strain, SC5314. In addition, the potential exists that Assembly 20 contains some regions where small contigs have been misassembled based on the WO-1 sequence data.

The Assembly 20 group is working to correct the sequence of these regions as quickly as possible. The Biotechnology Research Institute of the National Research Council of Canada has released a list of the regions affected. These regions are displayed in the Genome Browser in CGD, see example. A list of the regions and their chromosomal locations may be downloaded, and a list of the ORFs that are affected by the regions may be also be downloaded.

Update November 22, 2006: By comparing the 1kb flanking parts for each suspect region against the Contig19 sequences, CGD was able to reduce the size of many of the suspect regions. These changes are now reflected in the Genome Browser display, as well as in the downloadable files.

The physical mapping data are now available from the University of Minnesota, at http://albicansmap.ahc.umn.edu/index.html. The optical mapping data will be made available shortly. The mapping data, which were used to order and orient contigs, originate exclusively from the reference strain SC5314. These groups are working to revisit each of the gap/overlap regions and to correct the errors.

CGD continues to provide full access to Assembly 19. For situations where you need to ensure that you are working only with sequence from the reference strain SC5314, you may retrieve data from Assembly 19 instead of Assembly 20. Please feel free to contact us with any further questions. (Posted October 19, 2006, last updated November 22, 2006)

CGD usage: Half a million hits

The number of CGD database accesses has now passed 500,000 in total. As we celebrate this milestone, CGD would like to thank the Candida research community for your support. (Posted November 3, 2006)

Search for C. albicans ortholog of an S. cerevisiae gene

We have added a new option to the CGD Category Search. You may enter the Standard Name of an S. cerevisiae gene or genes, and the tool returns the C. albicans ortholog. (View an example query, CDC*.) To use this new search tool, select "S. cerevisiae ortholog" from the CGD Category Search menu on the Full Search page, $roortUrl/SearchContents.shtml. Special thanks to Judy Berman for suggesting this feature. (Posted September 27, 2006)

Assembly 20 of the C. albicans genome sequence

We are pleased to announce that Assembly 20 of the C. albicans genome sequence is now available at CGD. This new assembly was a collaborative effort of groups at the Biotechnology Research Institute of the National Research Council of Canada, the University of Minnesota, and Chiba University of Japan. Special thanks to Andre Nantel and Marco van het Hoog for providing sequence and annotation files to CGD.

Some highlights:

  • Get Assembly 20 sequence from the "Retrieve Sequences" menu on each Locus page (view example Locus page)
  • Browse Assembly 20 using the GBrowse Genome Browser, and see where contigs from Asssembly 19 align to chromosomes from Assembly 20 (view example)
  • Download Assembly 20 files: sequence files, and sequence alignments and analyses (see the Sequence Documentation page)
  • View Assembly 20 chromosomal coordinates on CGD Locus pages
  • BLAST Assembly 20 sequences
  • See the type of change, if any, that affected each ORF between Assembly 19 and Assembly 20 (under "Feature type" on each Locus page)
  • View the Chromosomal Features Table (see features flanking ACT1, for example) via the new "Maps and Displays" menu on each Locus page
  • Search for gene or chromosome sequence from Assembly 20 using the CGD Sequence Retrieval tool
  • Expanded content in the Locus/Feature History Notes section, linked off each Locus page (view example)
(Posted September 14, 2006)

Software improvements at CGD

We have upgraded the CGD infrastructure to increase the speed at which CGD Locus pages load in your web browser. Page loading and navigation within the GBrowse genome browser interface is now more rapid, and the latest version of the GBrowse software has been installed. (Posted July 31, 2006)

Links to Transcription Modules

CGD now contains links to the transcription modules, or sets of co-regulated genes, described by Ihmels et al. in "Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program." PLoS Genet. 2005 Sep;1(3):e39. To view the other genes that are co-regulated with any gene of interest, select the link entitled "Transcription Modules," which is located on the list of "External Links" near the bottom of each CGD Locus page. (Posted May 22, 2006)
We would like to hear your thoughts on some current issues at CGD. The CGD feedback form is here as a Word document for download. Please, fill it out and email back to CGD Curators. (Posted April 17, 2006)

Contig Sequence Retrieval tool

We have added a Contig Sequence Retrieval feature to our Sequence Retrieval tool. It is now possible to retrieve the sequence of a region between two coordinates on any contig by selecting the contig from the pull-down menu and entering the coordinates of the region you would like. To retrieve the sequence of an entire contig, leave the Beginning and End Coordinate boxes empty. To retrieve the reverse complement, enter the larger-numbered coordinate in the Beginning Coordinate box and the smaller-numbered coordinate in the End Coordinate box. The tool may be accessed using the "Get Sequence" link under "Search Options" on the CGD home page or from the Full Search page. Special thanks to Julia Koehler for suggesting this feature. (Posted April 5, 2006)

View BLAST results in GBrowse

The BLAST results page now contains a "CGD GBROWSE" hyperlink above each sequence match ("hit"), which opens the GBrowse genome browser with the hit displayed in the browser window. GBrowse may be used to further explore the region containing the match: to view ORFs and other features in the neighborhood of the hit, to browse and download adjacent sequences, to view the 6-frame translation of the region, and to view restriction sites. (For a more extensive description of GBrowse features, please see our GBrowse documentation page). Special thanks to Marc Logghe for suggesting this feature. (Posted March 10, 2006)

2005 CGD News Archive

 

Large-scale datasets archived at CGD

We have added an archive of large-scale datasets to our ftp site. The data are obtained from published and publicly accessible supplements. The files are in their original format as published or supplied by the authors. The archive can be accessed from the Download Data Index Page, or via the "and more" link under the Download Data heading on the sidebar. It is our intention to provide a single access point to results that are typically scattered over the Internet. Please, contact the CGD Curators if you want to contribute your results. (Posted December 22, 2005)

Candida Community Job Postings at CGD

A new community resource is now available at CGD. The Candida Community Job Postings page contains announcements of employment opportunities that are related to Candida biology. The page may be accessed using the link under Community Resources on the sidebar on the left-hand side of this page. To submit a posting, contact the CGD Curators. Postings will be added at the discretion of the CGD staff. Postings will typically remain on the CGD web site for two months after submission, or they may be removed sooner at the request of the submitter. (Posted November 29, 2005)

Download Data Index Page

The Download Data Index Page lists the files available for download from the CGD web site. The "and more" link under the Download Data heading on the sidebar leads directly to the Download Data Index Page. (Posted November 29, 2005)

Candida research community mourns Myra Kurtz

Myra Kurtz was a true pioneer in the field of Candida molecular genetics. A tribute by Aaron Mitchell, "Remembering Myra," has been posted on the Community News page. (Posted November 18, 2005)

Aliases from Assemblies 4 and 6

We have added a comprehensive set of gene name aliases from Assemblies 4 and 6 of the C. albicans genome sequence to CGD. The aliases now appear on the corresponding CGD Locus pages. In addition, the mappings may be downloaded in bulk (Assembly 4 to Assembly 19, README; Assembly 6 to Assembly 19, README). Special thanks to Judith Berman and Andre Nantel for helpful information. (Posted November 15, 2005)

Gene Ontology (GO) Usage survey

The Gene Ontology Consortium has developed a short online survey to help them improve their services to their user community, and help direct their resources more effectively, as well as to help them in the competitive renewal of their grant in the new year. CGD users are invited to participate, especially as the GO consortium wants to solicit more feedback from bench biologists. There is no requirement to submit your name or email address. To complete the survey, please go to: http://www.AdvancedSurvey.com/default.asp?SurveyID=32355. (Posted October 28, 2005)

New CGD BLAST tool

We are pleased to announce a new tool for conducting sequence searches of the C. albicans genome. CGD BLAST may be accessed using the "BLAST" link on the toolbar at the top of each CGD web page. Nucleotide and protein queries are available. BLAST queries may be conducted against several C. albicans data sets, including the archived assemblies 4, 5, or 6 as well as the current assembly 19 sequence. To query the sequence of a C. albicans gene against the rest of the genome, use the new "Sequence Analysis Tools" menu on the sidebar on the right-hand side of each Locus Page. Queries against sequences of other fungal genomes may be conducted using the Fungal Genomes Search tool at CGD. (Posted October 19, 2005)

Sequence assemblies archived at CGD

C. albicans sequence assemblies, including the older Assemblies 4, 5, and 6, have been archived at CGD. These data may be retrieved from the "archived_assemblies" folder on the CGD Sequence Download Page. (Posted September 6, 2005)

Orthology information for download

A table containing the mapping between C. albicans genes and their S. cerevisiae orthologs is now available for download in a tab-delimited text format. This orthology information has also been added to the CGD Chromosomal Feature file. In addition, the input files used and the output file generated by the InParanoid software are available for download from the CGD web site. (Posted September 1, 2005)

Links to S. cerevisiae orthologs added to CGD

CGD now includes links to S. cerevisiae orthologs of C. albicans genes. Ortholog gene names appear on the Locus Pages, directly below the Description section, and they are hyperlinked to the corresponding Locus Pages at the Candida Genome Database (CGD). The ortholog mappings were generated using the InParanoid software (version 1.35) developed at the Karolinska Institutet. The haploid complement of C. albicans proteins from CGD was compared to the latest set of S. cerevisiae proteins from CGD, and the latest set of C. elegans proteins from the Sanger Institute, wormpep 145, was used as an outgroup. Stringent cutoffs were set: BLOSUM80 (instead of the default BLOSUM62), and an InParanoid score of 100%. In total, 3594 ortholog mappings met these criteria. (Posted August 15, 2005)

External database links added to CGD

CGD Locus Pages now include a section entitled "External Links," which is located right above the "Additional Information" section at the bottom of each page. The hyperlinks may be used for direct navigation to the gene information pages for the Annotation Working Group data at the NRC-BRI, for CandidaDB at the Pasteur Institute, and for the Comprehensive Candida Genome Database at MIPS. (Posted August 8, 2005)

C. albicans genome annotation paper is published

The manual annotation of the Candida albicans genome by the Annotation Working Group is described in a new paper by B. R. Braun et al., entitled A Human-Curated Annotation of the Candida albicans Genome. The paper is published in the inaugural issue of PLoS-Genetics. (Posted August 2, 2005)

Codon usage table available

We have calculated the frequency of use of each codon in in the diploid complement of C. albicans protein-coding genes. There is a link to the table in the left-hand menu bar of the CGD home page, under the heading "Download Data". This document contains details on the method and a legend to the table, as well as the table itself. (Posted July 1, 2005)

Download Sequence Files

You may now download gzip compressed sequence files in bulk from the CGD Sequence Download page. There is a link to this page under Download Data on the left-hand sidebar of the CGD Home Page. DNA sequences are available with or without introns and upstream and downstream regions flanking each ORF. ORF translations (predicted protein sequence), full contigs, and sequences of non-ORF features are also available. More detail is found on the Sequence Documentation page and in the README file that accompanies the Sequence Download page. (Posted June 7, 2005)

C. albicans tRNA genes added to CGD

We have now added tRNA-encoding genes to CGD. These genes were predicted using the tRNAscan-SE algorithm developed by T. M. Lowe and S. R. Eddy. The names appear in the following format, which is based on the format of the S. cerevisiae tRNA gene names: a lower-case t (for "tRNA"), followed by the one-letter abbreviation of the amino acid with which it is charged, followed by the anticodon (in parenthesis) followed by an integer. The name of the corresponding allele has an additional ".2" suffix. For example, "tA(AGC)1" is an alanyl tRNA with an AGC anticodon, and "tA(AGC)1.2" is the corresponding allele.

The tRNAscan-SE algorithm predicts that there are 133 tRNA genes in the haploid complement of the C. albicans genome. To find all of the tRNAs in CGD, please use the following wildcard search:
t*(*)*

These tRNA genes also appear in the GBrowse genome browser. (Posted May 24, 2005)

New Sequence Retrieval Tool

You may use the Sequence Retrieval Tool to search for a gene or ORF and retrieve DNA or protein sequence. The tool allows you to select how much upstream and/or downstream flanking sequence to view. To access the tool, use the "Get Sequence" link under Search Options on the left-hand sidebar of the CGD Home Page or use the "Get Sequence" link under Specialized Gene and Sequence Searches on the Search Options page. Please see the Sequence Documentation page for more details. (Posted May 13, 2005)

DNA and Protein Sequence in CGD

We are pleased to announce that C. albicans sequence information is now available in CGD. DNA and protein sequence for any ORF may be viewed using the new "Retrieve Sequences" menu on the right-hand sidebar of any Locus Page. For more details, please see the Sequence Documentation page.

In addition, you may view and navigate the contigs from Assembly 19 of the genomic sequence using the GBrowse Genome Browser. GBrowse may be accessed using the "Contig Location(s)" links or the GBrowse map thumbnail views, which now appear on each Locus page.

See the ACT1 Locus Page as an example. (The maps will take a moment to load.) The two small maps on the right-hand side of the page correspond to the two ACT1 alleles. Clicking on one of these will display a region of the contig, with the selected ORF at the center and neighboring ORFs visible on either side. Near the bottom of the ACT1 Locus Page are links marked "Contig Location(s)." Clicking on one of these links will display a "zoomed-in" view of the ORF without flanking sequence. From either of these views, you may zoom in or out on any genomic region or navigate to a different region of the contig, display restriction sites or G-C content, view DNA or protein sequence, or take advantage of other GBrowse features, which are described on the GBrowse Help Documentation page. The GBrowse software was written by Lincoln Stein as part of the Generic Model Organism Database (GMOD) Project. (Posted April 25, 2005)

Candida labs page added

The link to the new Find Candida labs page has been added to the Community Resources sidebar. The page contains a list of research groups working on Candida, along with contact information and links to web pages, publications, and other data. The information comes directly from Candida researchers who have submitted their Colleague data to CGD. We invite Candida colleaugues to submit their lab information via the Colleague Submission form. (Posted April 4, 2005)

New Weekly Reports: CGD Curation News

The CGD News page now includes a link to our list of papers that have been added to CGD in the past week. We also list all of the papers in CGD that include Genome-wide Analyses. These lists will be updated every week. (Posted March 30, 2005)

Download CGD Information about C. albicans Genes

The CGD chromosomal_feature file is now available for download. This file contains the CGD gene names, orf19 names, other aliases, and the gene descriptions. The format of the file is described in the README document. To download the file, use the link under the Download Data heading on the CGD sidebar (on the left-hand side of this page), or click here. (Posted March 14, 2005)

Gene Ontology assignments from the Annotation Working Group

The Gene Ontology (GO) terms curated by the Candida albicans Annotation Working Group are now displayed in CGD. A total of 12916 new GO annotations have been added. The Annotation Working Group formed at the ASM Conference on Candida and Candidiasis in 2002. It consists of researchers volunteering their own time to annotate the genome; the entire Candida community is indebted to them for their efforts. Their work is described in a paper in press at PLoS Genetics, and is also online at the Candida albicans pages web site at the Biotechnology Research Institute of the National Research Council, Canada. (Posted February 14, 2005)

Gene Ontology evidence codes displayed on CGD Locus Pages

The Gene Ontology (GO) evidence codes are now displayed on the CGD locus page. Previously, the GO evidence codes were displayed only on the GO Details page, which is accessed using the GO Evidence and References link on the Locus Page. Now the evidence codes are displayed in both places. A detailed explanation of the evidence codes and their use is found on the GO Consortium website. (Posted February 14, 2005)

New Community Resource: Candida Gene Disruption Set

Aaron Mitchell's and Bill Nierman's labs have created Tn7-UAU1 transposon insertions in 4170 unique C. albicans ORFs, and they are offering these clones to the community (up to 20 clones per laboratory, free of charge). For more information on the project, including how to request clones, please see our CGD Community News page. (Posted February 10, 2005)

CGD paper is published in Nucleic Acids Research

A paper describing the Candida Genome Database has been published in the Nucleic Acids Research 2005 Database Issue. The paper, which is entitled "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information," is available online in HTML or PDF format. (Posted January 3, 2005)

2004 CGD News Archive

 

CGD GO Annotations File is now available

We are pleased to announce that all of the CGD Gene Ontology (GO) curation is now available for download. To download this file, use the link under the new Download Data heading on the CGD sidebar (on the left-hand side of this page), or click here. This CGD GO Annotations File is updated daily to reflect the very latest curation in CGD.

"GO annotations files" are sometimes called "gene associations files." The CGD file is described in detail in our README document. This GO Annotations File file uses the standard file format defined by the GO Consortium. (Posted November 17, 2004)

CGD Gene Registry is now available

CGD is ready to provide a gene name registry for the Candida research community. As agreed by the community at the ASM Conference on Candida and Candidiasis in March 2004, all new genetic names for C. albicans genes should be reserved through the gene registry before publication. An online gene registry form is now available. A link to this form can be found under the Submit Data heading on the left-hand side of this page. Gene nomenclature guidelines are also available online. (Posted November 12, 2004)

CGD Colleague Registry is now available

CGD is ready to serve as a directory for the Candida research community. You may submit information about your research interests, and contact information, to CGD using the Colleague Submission/Update form. All information submitted is publicly searchable (by surname) via the CGD category search. (Posted September 7, 2004)

Announcing the Candida Genome Database

CGD is now available online. The menu on the left-hand side of this page provides links to search options, tools, and additional information.

At this time, CGD contains more than 900 gene product description lines, and approximately 1,500 mutant phenotype descriptions and 1,500 Gene Ontology (GO) term assignments, all based on literature curation.

CGD literature curation is an ongoing project. In the future, CGD will contain comprehensive curation of the C. albicans literature. To start, CGD curators have been focusing on one or a few references that describe each gene. CGD curators read the full text of each paper if it is available. In some cases, only the abstract has been curated. The reference lists were initially generated using an automated search of the PubMed database at NCBI, and these search results were then manually screened to eliminate spurious references. CGD curators are also conducting a manual review of the C. albicans literature to identify papers that may not have been identified during the automated screen.

The C. albicans genomic sequence data is scheduled to be added to CGD in Fall 2004. Once this information has been incorporated, CGD will provide access to sequence analysis and visualization tools similar to those available at CGD. Also coming soon to CGD are links between CGD and CGD locus pages, which will provide instant access to information about the S. cerevisiae orthologs of C. albicans proteins.

We welcome your comments and suggestions. Please feel free to contact us and let us know how we can better serve the C. albicans research community. (Posted August 13, 2004)

Candida Genome Database will be online August 15

We are pleased to announce that we will have the first version of CGD available on this web site by mid-August. CGD will contain over 700 gene product descriptions, 1350 Gene Ontology (GO) term assignments, and 1550 phenotype descriptions, which have been gathered from the published literature by the CGD curators. We are currently beta-testing our database software, and we look forward to having the database online and available for your queries within the next few weeks. (Posted July 28, 2004)

C. albicans genome sequence publication now available

A publication describing the C. albicans genomic sequence, from the Candida sequencing project group at the Stanford Genome Technology Center, has just appeared in PNAS:

Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S.
The diploid genome sequence of Candida albicans.
Proc Natl Acad Sci U S A. 2004 May 11; 101(19): 7329-7334.

The sequence paper is available here. (Posted May 12, 2004)

Preliminary C. albicans gene name reservation system available

In response to requests from researchers, we will begin to collect reservations for C. albicans gene names. Please contact CGD if you are thinking of naming a new gene. (Posted April 22, 2004)

C. albicans genetic nomenclature guide available

We have posted a nomenclature guide for C. albicans gene, allele, and protein names, including tips on choosing new C. albicans gene names. Many thanks to the members of the Annotation Working Group and its advisory committee for reviewing these guidelines. (Posted April 9, 2004)

CGD discussed at ASM Conference

The CGD project was presented to the Candida community at the ASM Conference on Candida and Candidiasis, held March 18-22 in Austin, Texas. A review of the meeting, written by Joy Sturtevant, is available here. Community input on the CGD project was sought through a survey distributed to participants and through informal discussions.

At the Annotation session, which was attended by approximately 150 researchers, the community was asked whether CGD should serve as the C. albicans gene name registry, analogous to the role that CGD plays in the S. cerevisiae community (see the CGD gene naming guidelines). By a show of hands, the attendees were unanimously in favor of this. Among 75 surveys that were returned, 74 indicated that CGD should serve as the gene name registry. (One survey indicated that it should not, but gave no explanation.)

Given this community mandate, we will establish a gene name reservation system as soon as possible. In the very near future, we will post guidelines for the format of C. albicans gene names.

In addition to asking about the gene name registry issue, the survey asks for opinions on what features would be most useful in CGD. The design of CGD will be determined by community needs. To take a survey by email, please contact CGD. (Posted March 25, 2004)


CGD project to start April 1, 2004


A project to create a freely accessible community database for genomic, gene, and protein information for Candida albicans will begin on April 1, 2004. We hope to be online by the end of July 2004.

The genomic sequence on which CGD will be based is assembly 19 of the C. albicans sequence. This assembly is the accumulation of much thoughtful, difficult work by the Candida sequencing project group. (For more information or to download the sequence, see the Candida sequencing group's Release Notes page.)

CGD will incorporate the annotation of Assembly 19 generated by the Annotation Working Group. This group, formed at the ASM Conference on Candida and Candidiasis held January 13-17, 2002, in Tampa, FL, consisted of researchers volunteering their own time to annotate the genome; the entire Candida community is indebted to them for their efforts. The group has completed the manual annotation of 6484 confirmed ORFs based on version 19 of the genome assembly.

CGD curators will correlate genomic sequence information with the annotation generated by the Annotation Working Group and with information curated from the literature. CGD will be based on the database architecture of the Candida Genome Database (CGD) and will be interlinked with CGD. We hope that, like CGD, CGD will develop with extensive input from the research community. We appreciate receiving all comments, suggestions, or questions from Candida researchers. To contact CGD, send email to the CGD curators. (Posted March 12, 2004)


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