What's New in SGD in 1997

November 21, 1997

• SGD releases SacchDB version 4.10, using the ACEDB software (version 4.5) developed by Richard Durbin and Jean Thierry-Mieg. SacchDB version 4.10 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.]
• An improved Yeast Genome Pattern Matching program is available. This program allows you to use ambiguous characters in your searches and will tolerate mismatches, insertions or deletions.

October 28, 1997

• Commonly Used Auxotrophic Markers are in a table form with names, molecular descriptions, phenotypes and references. The data was obtained from Brachmann et al., 1998.

October 3, 1997

• Global Gene Hunter now has two additional query options. The first is a search of the Protein Information Resource (PIR), which provides information about protein sequences. The second is a search of the American Type Culture Collection (ATCC) catalog, to provide access to information about yeast strains and clones.

September 29, 1997

• The SGD WWW pages have been re-organized in response to user comments. The column on the left-hand side is now constant and lists all the major pages: Search SGD, Sequence Analysis & Tools, Maps, Literature, Gene Registry, Lists & Tables, General Yeast Information, Help, Meetings, Submit Data & Contact SGD, and About SGD. Each of the major pages now has its options listed and explained in the main body of the page.
• SGD BLAST results now have a small graphic to aid you in determining the position of your "hits" with respect to your input sequence. Clicking on each hit will show you the actual sequence alignments.
• Yeast Homology to Mammals: A new SGD feature for examining the relatedness between yeast and mammalian protein sequences is described in the recent article "Yeast as a Model Organism", Science 277:1259.

September 8, 1997

• An improved SGD Colleague Submission/Update Form allows you to search for and to edit your existing entry, line-by-line. [Note (11/21/02): This form has since been replaced by an even newer SGD Colleague Submission/Update form].
• In response to decisions made at a special session of the 1997 CSH Yeast Cell Biology Meeting, the SGD Gene Naming Guidelines have been modified. Gene name reservations now extend for a full year. In addition, a sequence submission to GenBank will no longer qualify to "lock in" a gene name.
• The new version of Genomic View allows you to display not only the Chromosomal Features Map, but also the Physical Map and the Combined Physical and Genetic Map.
• The name of the "DNA Sequence Retrieval Form" has been changed to the "DNA/Protein Sequence Retrieval." Other changes to the form include making the amount of upstream and downstream sequence retrieved default to zero basepairs, removal of introns from spliced ORF sequences, and a "No Header" display option for all sequence retrievals.
• The SGD Gene Name List, the ORFs Locations Table, and the non-ORF Features Table have been updated and will now be kept current with the information in the database. [Note (11/21/02): All of these tables are now obsolete; for current information, please see Anonymous FTP and select "data_download."]

July 10, 1997

• You can now use Pattern Matching to search for patterns in sequences upstream of ORFs. You can search 500 basepairs, 1000 basepairs or 2000 basepairs of upstream untranslated region.
• Genomic Stripe View allows you to look for repeats of the sequence of your choice. This tool uses comparison matrices to display all the regions in the genome with similarity to a given sequence. Using pre-calculated matrices of similarities for the whole genome, you can display the similarities of a small (or large) slice of the genome. Genomic Stripe View is available as a display option for Gene/Sequence Resources.

June 4, 1997

• A list of all the chromosomal tRNAs, their systematic names, their chromosomal coordinates and access to their sequences is available in the tRNAs from SGD table. Additional option of retrieving and displaying the tRNA sequences using Gene/Sequence Resources.

May 31, 1997

• An experimental Java version of the Genomic View is available to SGD users. This interactive display allows you to use a pull-down menu to determine whether to display a section of genomic sequence in the Features Map format, the Physical Map format (showing overlapping ATCC clones) or the Combined Physical and Genetic Map. Your feedback is welcome. Please e-mail us at yeast-curator@genome.stanford.edu.
• SGD has introduced a new tool for finding and displaying DNA sequences, called SEQ and Display. This program allows you to obtain sequence information or view a variety of different genetic and physical map displays for all the DNA sequences in the database. You can search by gene name, ORF name, sequence name or chromosome coordinates.
• The Pattern Matching program is available from Sacch3D. With Pattern Matching, you can search for small patterns within the yeast genome. This is ideal for searches with sequences that are degenerate or are too small for the BLAST or FASTA forms. Currently, the search is limited to the DNA sequences or protein translations of defined ORFs. There is also a useful Help: Pattern Matching document.
• The Sequence Similarity View allows you to examine regions of similarity within the Saccharomyces cerevisiae genome. This program uses a matrix to calculate similarities and the results can be visualized by zooming in and zooming out. The Sequence Similarity View Tutorial is the topic of SGD'S HOT TIP for May 30, 1997.
• The new SGD Directory provides an organized listing of all our standard Web pages, forms and programs. This useful tool helps you navigate the SGD Web site. This page is no longer available. It has been replaced by the site map. (November, 2002).
• The Lists & Tables Web page consolidates our FTP sites, tables and lists into one easy-to-find reference page. This page is no longer available. It has been replaced by the new Download Data contents page. (November, 2002).

April 10, 1997

• SGD introduces the "Guide to Saccharomyces Genome Database," a list of the most common uses of and questions about our project. You can consult this document to find new uses of the database, or to answer some of your questions about the information contained in the database. The guide is organized into seven topics called "Gene Information, References, and Registration," " Searching SGD,," "Sequence Information and Tools," "Map Information," "External Information -- Other Databases or Laboratories," "Help, Tutorials, and News," and "Contacting Other Yeast Researchers and SGD." This page is no longer available. It has been replaced by the site map. (November, 2002).
• SGD curators have compiled a "List of Handy SGD URLs" to help you navigate the database. These include all the URLs mentioned in the "Guide to Saccharomyces Genome Database." This page is no longer available. It has been replaced by the site map. (November, 2002).

April 8, 1997

• The NotFeature Dataset has been made available for FASTA searches. This dataset includes only non-coding DNA. It was generated by subtracting all identified genetic features (ORFs, tRNAs, RNA genes, centromeres and Ty transposons) from the genomic DNA sequence.
• The NotFeature Dataset is available via FTP in FASTA format. Please consult the README file.

March 12, 1997

• SGD Hot Tip on Viewing the Combined Physical and Genetic Maps: This Hot Tip highlights SGD's side-by-side representation of the Physical and Genetic maps of S. cerevisiae.

March 1, 1997

• Release of SacchDB Version 4.7: SGD has made available a new public release of SacchDB using the ACEDB software (version 4.3) developed by Richard Durbin and Jean Thierry-Mieg. SacchDB version 4.7 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 27, 1997

• SGD has created a new dataset for BLAST searches called "NotFeature." This is the ideal dataset for searching for very small, uncharacterized open reading frames or regulatory regions. It contains all the genomic DNA that is NOT a genetic feature (i.e., an ORF, tRNA, RNA gene, centromere or Ty element).

February 12, 1997

• SGD has added a comprehensive set of tRNA sequences that have been given systematic names. See the tRNA naming conventions for an explanation of the format of the systematic names. All the tRNAs are available both as sequences an as clone objects in the physical map.
• A subset of the full-length Ty transposons and their LTRs have been added to the database. The Ty sequences were identified with the generous help of the Dan Voytas laboratory. All the Tys and LTRs have been added for chromosomes I, VI, VIII, IX, X, XI, XII, XIII, XIV, XV and XVI. Ty elements for the remaining five chromosomes will be added to the database soon. In collaboration with the Voytas group and their colleagues, the Tys were given systematic names. For an explanation, see the Ty naming guidelines. The Tys and the LTRs are available both as sequence objects and as clone objects.
• The Chromosomal Features Graphic and Table now show more genetic features. Full-length Ty transposons, LTRs, tRNAs, rRNAs, snRNAs and RNA genes are now indicated by a color code or description. As before, these elements are charted along with the nearby ORFs, so you can see their relative locations and distributions. For an example, see the graphic or table for a region of Chromosome VIII.
• The Chromosomal Features Table now has a short description associated with every locus. These descriptions were created by using SGD gene_product information from the locus page, Brief_identification from the sequence page, or description from the locus page. For an example, see a region of Chromosome V.
• The Combined Physical and Genetic Maps of S. cerevisiae now have a calculation of the ratio of centimorgans to kilobasepairs for each chromosome. It is located at the bottom of the page. Keep looking here for the announcement of a page with the same ratio calculated for every genetic interval of each chromosome.

January 27, 1997

• New SGD Homepage: We now offer a streamlined homepage to assist users in navigating the SGD services. Important announcements are included in the body of the page, while standard destinations are offered in a column at the left of the page. This new look has been extended to several of our other pages as well, including the SGD Search Form.
• SGD Help Index: The Help index provides a guide to all the on-line SGD help documents. The index includes What's New, Hot Tips, the SGD Glossary, and Gene Naming Guidelines as well. The SGD Help Index is no longer available. Links to Hot Tips and the SGD Glossary can now be found on the Help Resources contents page. The link to Gene Naming Guidelines can be found on the Submit Data contents page. (November, 2002)
• New searches added to Global Gene Hunter: Global Gene Hunter now will search for a S. cerevisiae gene name in Sacch3D, Swiss-Prot, MIPS and in addition to SGD, GenBank and PubMed. The default search is for all the sites, but you can easily determine where you would like to direct your search.