What's New in SGD in 2002

November 25, 2002

• Over the years, SGD has developed new resources that have allowed our users to perform comparative, functional, and large-scale analyses of the yeast genome. Some of the recent additions have been the GO Term Mapper, the GO Term Finder, Protein pages, and the Synteny Viewer to view fungal aligments. In order to provide easier access to these new resources and to current SGD pages, the SGD site has been reorganized and given a new look. The new features of the SGD reorganization are highlighted here. Please contact SGD if you have any questions or comments.

November 22, 2002

• Open Biosystems is now a distributor of the Yeast Knockout sets constructed by the Saccharomyces Genome Deletion Project Consortium. All clones can be queried online, and complete product information on parental strains, clones, and collections is available.

November 12, 2002

• The phenotype results from the Systematic Deletion Consortium ((Giaever er al., 2002 Nature 418:387-91)) Nature 418:387-91) have been incorporated into SGD. In addition to the viability assay that was previously added to SGD, results from experiments testing growth on NaCl, nystatin, galactose, sorbitol, pH 8, minimal media, and synthetic complete media are now available.

October 4, 2002

• Every S. cerevisiae protein is now associated with a biological process term (or terms) from the Gene Ontology (GO).

September 23, 2002

• In response to feedback from our users, we have developed a new option for viewing SGD locus pages. This single page view serves as an alternative for those who prefer scrolling through a long page, versus the traditional SGD locus page, where you click to find more detailed information. To reach the single page view option, click on the Alternative single page format link at the top of any SGD locus page.

September 17, 2002

• A new Gene Ontology (GO) tool called the GO Term Finder has been developed at SGD. This tool helps you find what a group of genes may have in common. For more information, please go to the SGD help page for this tool. In addition, a new graphic display for viewing the GO structure has been incorporated in the GO Term Finder and GO Term Mapper results, as well as the GO term pages themselves.

September 16, 2002

• SGD adds the initial results of the genome comparison between S. cerevisiae, S. castelli, and S. Kluyveri. These results are kindly provided pre-publication by Paul Cliften and Mark Johnston. You can view ClustalW alignments of the orthologous proteins by choosing the "Fungal alignments" option under the Comparison Resources menu on the locus page.

September 16, 2002

• Update: Link to the genome wide alignments between S.cerevisiae and S.paradoxus, S.mikatae, and S.bayanus on the locus page has been changed from "Other budding yeasts homologs" to "Synteny Viewer" to more accurately describe the link.

August 14, 2002

• SGD has created a tutorial to familarize users with the Gene Ontology (GO) and how it is used at SGD. The tutorial gives an overview of GO and highlights pages and tools at SGD that use GO annotations. In addition, the tutorial provides links to other sites that may help users take advantage of the power of GO. For more information about GO, see the GO home page or the SGD help page for GO.

August 13, 2002

• Predicted protein properties such as molecular weight, pI, CAI, protein length, etc. for all S. cerevisiae ORFs are available on the SGD ftp site, in the protein_info/ directory.

July 29, 2002

• SGD released a graphical sequence alignment viewer to display the results of genome wide comparsions between S. cerevisiae and S. paradoxus, S. mikatae, and S. bayanus. On August 9, 2002, Clustal W protein alignments were added as a link from the graphic display.

July 29, 2002

• SGD now provides a tool, the GO Term Mapper, that maps the granular GO terms used to annotate a list of genes to their more general parent terms (ie. GO Slim terms). This tool allows you to look at broad biological processes, molecular functions, or cellular components in which a list of genes is involved or localized.

July 23, 2002

• SGD now links from each locus page to the GRID database of genetic and physical interactions.

July 16, 2002

• SGD is now hosting VectorDB, generously provided to us by Stephen Misener. VectorDB contains annotations and sequence information for several yeast/E.coli vectors as well as other vectors commonly used in molecular biology. On vector description pages, there are links to GenBank sequences, allowing you to easily retrieve the sequence of the vector. You can search for information for more than 2600 vectors with the VectorDB search and BLAST tools.

July 15, 2002

• The ftp site has been reorganized so that it is easier for users to find the data that they need. In addition, previous versions of files will be stored in an archive/ directory so that changes can be tracked.

April 25, 2002

• Sequence data is now stored in the SGD Oracle database, allowing for faster retrieval and better archiving of sequences. In addition, there are links on the sequence display for retrieving other sequence formats (FASTA, GCG).

April 25, 2002

• A new Protein Info and Composition page is now available at SGD. This page provides basic information about a protein sequence, and also has links to tools such as hydropathy plots, helical wheels, etc.

March 27, 2002

• A new display for clone information is now available at SGD (see for example the clone page for Wash U clone 7082).

March 26, 2002

• The names of Saccharomyces cerevisiae TAF genes have been changed to reflect the nomenclature agreed upon and published in Tora L (2002) A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev 16(6):673-5; this paper explains the changes and includes a tables with old and new gene names for S. cerevisiae, H. sapiens, D. melanogaster, C. elegans, and S. pombe. Links to the TAF genes in SGD can be found here.

March 15, 2002

• The text search option from the Full Search page now queries the Oracle database. Fields queried include gene names, aliases, Gene Ontology (GO) terms, colleague and author names, paragraph text, paper abstracts, general descriptions, and phenotypes.

February 7, 2002

• The results of the systematic deletion project have been updated; 43 additional genes were identified as being essential.

February 6, 2002

• SGD now provides links to the CandidaDB for Saccharomyces genes that have Candida albicans homologs. These links were generated by BLAST analysis done by the CandidaDB group at the Pasteur Institute.

January 30, 2002

• SGD has developed a new tool that links all associated sequences for any gene from its locus page. This tool searches multiple databases including GenBank, SwissProt, MIPS, PIR, and YPD and lists all appropriate sequences found in these databases along with the systematic sequence stored in SGD.

January 6, 2002

• The 2002 Yeast Genetics and Molecular Biology Meeting will happen this July 30-August 4 at the University of Wisconsin, Madison. The call for Abstracts, including all meeting information and forms, will be available on the Web around January 11. The call for Abstracts will not be sent via postal mail, it will be available only on the Web.

January 1, 2002

• Nucleic Acids Research 2002 Database Issue: SGD details how it provides secondary gene annotation using the Gene Ontology (GO) in it's publication in this NAR issue (Dwight et al. 2002. Nucl. Acids Res., 30(1):69-72).