New and Noteworthy

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)

• C. albicans Genome Snapshot.
• C. glabrata Genome Snapshot.
• C. parapsilosis Genome Snapshot.
• New papers added to CGD this week.
• View Genome-wide Analysis papers in CGD.

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)

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)

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)

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