What's New in SGD in 1998

December 11, 1998

• SGD presents a website, SGD Worm-Yeast Protein Comparison that is the companion to Chervitz, et al., 1998. Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence. Science 282:2022-2028.

December 4, 1998

• SGD has added a link to the Yeast Cell Cycle Analysis Project detailing the study by Spellman, et al. (Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization (1998) Molecular Biology of the Cell 9, 3273-3297).

December 3, 1998

• SAGE data from Velculescu, et al., (1997) Cell 88:243-251 is available via anonymous ftp.

November 20, 1998

• A table of 27 new ORFs added by SGD based on its analysis of the SAGE data of Velculescu, et al., (1997) Cell 88:243-251. It includes links to relevant information about each ORF and the data used to identify it.

November 9, 1998

• A list of yeast introns provided by the Ares Lab at the University of California, Santa Cruz is now available.

September 14, 1998

• Graphic and tabular versions of the Meiotic Double-Stranded Breaks on Chromosome III data of A. Nicolas and F. Baudat (Proc. Natl. Acad. Sci. USA 94:5213-5218) are now available.

August 14, 1998

• Deletion strains created by the Saccharomyces Genome Deletion project are available via Research Genetics. There are currently 676 ORF deletions available, with deletions on chromosomes I, V, VIII, XIII and XV.

July 27, 1998

• SGD has developed a method to query SAGE tags. SAGE tags are DNA sequences that have been shown to be expressed by Velculescu, V.E., et al. (Characterization of the yeast transcriptome (1997) Cell 88:243-251).

July 6, 1998

• The program and abstracts for the Yeast Genetics and Molecular Biology Meeting are now available. The abstracts can be searched by keywords or by concepts. The meeting will be held at the University of Maryland, College Park, from Tuesday, July 28, through Sunday, August 2.

June 25, 1998

• Using Gene/Sequence Resources: SGD curators have written a tutorial to show users how to use Gene/Sequence Resources to retrieve DNA and protein sequences, homologies, restriction maps, biological information and more.

June 19, 1998

• Global Gene Hunter has been modified to allow you to search SGD, GenBank and PubMed for gene name aliases that are known to SGD.
• Finding an ATCC Clone That Overlaps a Gene: SGD has updated this Hot Tip to show how the use of new SGD software (Gene/Sequence Resources) makes it simple to identify an ATCC clone that contains a sequence of interest.

May 7, 1998

• Gene/Sequence Resources is a new tool that serves as a central jumping-off point for obtaining information on your gene or sequence of interest. It replaces our previous "Seq and Display". You provide Gene/Sequence Resources the name of your gene or sequence, chromosomal coordinates, or raw DNA or protein sequence, and then click submit. Gene/Sequence Resources will then present a list for all the available options at SGD for analyzing or displaying information about that gene or sequence. Even better, Gene/Sequence Resources will save you time by automatically pasting in sequences when performing BLAST or other analyses, and it will take you to the standard name for a gene when you type in an alias. Bookmark this page and save time.
• The Genome-wide Protein Similarity View allows you to display all the ORFs in the S.cerevisiae genome that display similarity to one or more input ORFs. You can enter ORF names or gene names and access graphic or table displays of S. cerevisiae ORFs that demonstrate similarity based on a genome-wide Smith-Waterman sequence analysis.

March 12, 1998

• PubMed searches via SGD now permit the option of "exploded" searches that take advantage of NCBI MeSH terms. This may result in a larger number of PubMed search results than if you were to perform an "unexploded" search.

March 10, 1998

• You can now search DNA sequences upstream of coding regions using SGD's UTR (untranslated regions) datasets. The three datasets include the DNA sequences that are 500, 1000, or 2000 basepairs upstream of all defined ORFs in the systematic S. cerevisiae genomic sequence. The UTR datasets are available for BLAST, FASTA and PatMatch searches.

March 9, 1998

• SGD releases SacchDB version 4.11, using the ACEDB software (version 4.5) developed by Richard Durbin and Jean Thierry-Mieg. SacchDB version 4.11 is available for UNIX systems. Although SGD recommends using the WWW version of our database (it is more frequently updated and contains information that is unavailable in SacchDB), you can download a copy of the SacchDB database using Anonymous FTP [Note (11/21/02): SacchDB is no longer available via ftp (see obsolete SacchDB FTP site; for downloading data from the current database, please see Anonymous FTP available on our Download Data page).

February 10, 1998

• SGD has adopted a new nomenclature for the cytoplasmic ribosomal protein genes, as proposed in W. H. Mager, R. J. Planta, J.-P. G. Ballesta, J. C. Lee, K. Mizuta, K. Suzuki, J. R. Warner and J. Woolford (Nucleic Acids Res. 25(24):4872-4875).

February 6, 1998

• SGD has reorganized some of its WWW pages to emphasize information about and from the yeast community. Please refer to our new page, Yeast Community Information page. This page is no longer available. It has been replaced by the new Community Information page. (November, 2002)
• A new tool has been added to SGD's set of programs for sequence analysis! The Yeast Genome Restriction Analysis allows you to perform a restriction analysis on a input sequence or the sequence of an ORF, gene, clone or GenBank sequence you identify by name.

February 2, 1998

• The SGD BLAST search has been modified to use the "dust" filter by default for nucleic acid query searches. The dust filter masks out simple repeat and high AT rich regions from the query sequence. The resulting sequences contains Ns at the masked positions. This masking or filtering allow the search to go faster and possibly report more relevant hits. With all the simple repeats removed you can more easily see hits of the unique regions of your sequence. If you wish to turn the filtering off, just select "none" from the Filter Options menu on the BLAST form.
• SGD has assumed the responsibility for maintaining the list of Saccharomyces cerevisiae lab URLs. The list, Links to Saccharomyces cerevisiae Labs was maintained by Ramon Tabtiang in the Herskowitz lab until February 1998. Many thanks to Ramon for such a great resource!

January 1, 1998

• The NAR database issue features a paper contributed by the SGD staff that details some of out latest improvements and innovations. See: Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database.