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2008 CGD News Archive
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 Batch search
for S. cerevisiae orthologs and best hits now available
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S. cerevisiae orthologs and best hits
can now be searched for mutiple
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)
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Links to C. dubliniensis orthologs now available
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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 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)
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Updated
comparisons to S. cerevisiae
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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)
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New
Files Available for Download
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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)
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CGD User Survey
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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)
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New Links from CGD Locus Pages
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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)
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Candida Biochemical Pathways are now available at CGD
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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)
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2007 CGD News Archive
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New Features at CGD
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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)
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DSHB-Microbe: a monoclonal antibody resource for the microbial research community
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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)
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New Release of CandidaDB
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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)
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Assembly 21 of the C. albicans genome sequence
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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)
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Download directories restructured for easy
navigation
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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)
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Links to Fungal Orthogroups Repository web site
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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)
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Candida
albicans SNP data from Forche et al. available on
CGD GBrowse
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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)
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Optical Mapping Data Available
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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)
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9th ASM Conference on Candida and Candidiasis
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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)
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Intron data from Mitrovich et al. in CGD
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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)
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Candida
GO Slim
added
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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)
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New Community Resource: Candida albicans microarrays
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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)
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Assembly 21 Sequence Files
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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)
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S. cerevisiae Best Hits
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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)
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CGD paper published in Nucleic Acids Research Database Issue
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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)
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2006 CGD News Archive
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View changes across genome assemblies in the Genome Browser
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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)
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Recent additions to CGD
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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)
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WARNING: Assembly 20 Sequence Advisory
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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)
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CGD usage: Half a million hits
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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)
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Search for C. albicans ortholog of an S. cerevisiae gene
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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)
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Assembly 20 of the C. albicans genome sequence
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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)
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Software improvements at CGD
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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)
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Links to Transcription Modules
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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)
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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)
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Contig Sequence Retrieval tool
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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)
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View BLAST results in GBrowse
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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)
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2005 CGD News Archive
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Large-scale
datasets archived at CGD
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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)
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Candida Community Job Postings at CGD
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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)
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Download Data Index Page
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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)
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Candida research community mourns Myra Kurtz
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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)
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Aliases from Assemblies 4 and 6
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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)
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Gene Ontology (GO) Usage survey
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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)
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New CGD BLAST tool
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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)
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Sequence assemblies archived at CGD
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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)
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Orthology information for download
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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)
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Links to S. cerevisiae orthologs added to CGD
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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)
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External database links added to CGD
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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)
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C. albicans genome annotation paper is published
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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)
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Codon usage table available
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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)
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Download Sequence Files
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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)
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C. albicans tRNA genes added to CGD
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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)
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New Sequence Retrieval Tool
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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)
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DNA and Protein Sequence in CGD
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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)
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Candida
labs page added
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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)
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New Weekly Reports: CGD Curation News
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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)
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Download CGD Information about C. albicans Genes
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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)
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Gene Ontology assignments from the Annotation Working Group
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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)
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Gene Ontology evidence codes displayed on CGD Locus Pages
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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)
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New Community Resource: Candida Gene Disruption Set
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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)
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CGD paper is published in Nucleic Acids Research
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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)
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2004 CGD News Archive
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CGD GO Annotations File is now available
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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)
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CGD Gene Registry is now available
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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)
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CGD Colleague Registry is now available
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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)
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Announcing the Candida Genome Database
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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)
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Candida Genome Database will be online August 15
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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)
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C. albicans genome sequence publication now available
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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)
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Preliminary C. albicans gene name reservation system available
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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)
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 C. albicans genetic nomenclature guide available
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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)
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CGD discussed at ASM Conference
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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)
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CGD project to start April 1, 2004
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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 candida-curator@genome.stanford.edu. (Posted March 12, 2004)
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Note: The Candida Genome Database provides information about the molecular biology of the yeast Candida albicans to researchers. CGD staff are not physicians and cannot give medical advice. Information about pathogenic yeast infections such as candidiasis can be found online in the PubMed database or at the Candidiasis information page at Medline Plus.
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