PubMed Nucleotide Protein Genome Structure Taxonomy

Saccharomyces cerevisiae genome data and search tips Revised May 21, 2008

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Saccharomyces cerevisiae (baker's yeast), and the search tips specific to that organism. You can also return to the Saccharomyces cerevisiae genome view search page. The Map Viewer home page allows you to search the genome data of any organism represented in MapViewer.

  1. Scope of Data
  2. Available Maps
  3. Constructing queries
  4. Constructing URLs

Scope of Data back to top

The Map Viewer provides a view of Saccharomyces cerevisiae data from a variety of sources, including sequence-based and genetic maps, described below.

Saccharomyces cerevisiae Genomic Sequence Data back to top

The Saccharomyces cerevisiae strain S288c genome sequence, assembly, and annotation displayed in Map Viewer (build 2.1) is provided by the Saccharomyces Genome Database (SGD). An international consortium completed the sequencing of the Saccharomyces cerevisiae genome in 1996. SGD collects and maintains updates to the sequence and annotation.

The Saccharomyces cerevisiae S288c genome was the first eukaryotic genome to be completely sequenced. The sequencing and analysis of this genome is described in Goffeau A et al. Science 274(5287):546, 563-567, 1996.

BLAST of Saccharomyces cerevisiae Genomic Sequence back to top

The complete set of Saccharomyces cerevisiae sequence databases available for BLAST searching is shown on the Saccharomyces cerevisiae BLAST page, which includes a link to the database descriptions. In addition, those interested in comparative genomics can use the fungi genomes BLAST page, which allows BLAST searching of sequence databases for a number of other fungi either individually or in combination.

Additional Saccharomyces cerevisiae Genome Resources back to top

In addition to the Saccharomyces cerevisiae data available in the Map Viewer and through BLAST, Saccharomyces cerevisiae genome information can be accessed using the Entrez Genome Project Database. The Saccharomyces Genome Resources page, which includes links to Saccharomyces-related resources from NCBI and external sites, is another resource for information pertaining to Saccharomyces cerevisiae. In addition, the NCBI Handbook includes a series of exercises that demonstrate additional questions that can be answered with Map Viewer.

Available Maps back to top

The available maps for Saccharomyces cerevisiae include:

Genetic Linkage Maps back to top

Genetic Shows the genetic linkage data that were provided by the Saccharomyces Genome Database (SGD) via ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/genetic_map.tab. For more information about the source of the genetic linkage map, see the Description in SGD's Help document.

Sequence-Based Maps back to top

Clone Shows the yeast clones from M. Olson and L. Riles at Washington University in St. Louis (WashU) aligned to the chromosome sequence. Each clone is labeled with its American Type Culture Collection (ATCC) clone name (when available) or its WashU clone name, and links to the Saccharomyces Genome Database (SGD). The clone data is provided by SGD via ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/clone.tab.

Contig

Shows the complete assembled chromosomes. The chromosome sequences, which have RefSeq NC_###### accessions, are provided by the Saccharomyces Genome Database (SGD).

Genes Shows the gene annotations provided by the Saccharomyces Genome Database (SGD) on the chromosome sequence.

Genes shown on the left of the gray line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down). The Genes map presents a flattened view of all the exons in a gene. For example, if two splice variants are predicted for a given gene, and one splice variant uses exons 1, 3, 4 and the other splice variant uses exons 2, 3, 4, the Genes map shows exons 1, 2, 3, 4.

Saccharomyces bayanus MCYC 623 Shows the Saccharomyces bayanus MCYC 623 whole genome shotgun (WGS) contigs from WGS project AACA00000000.1 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AACA00000000 was submitted to GenBank/EMBL/DDBJ by the Broad Institute.

When the Saccharomyces bayanus MCYC 623 map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., MCYC 623).

Saccharomyces bayanus 623-6C Shows the Saccharomyces bayanus 623-6C whole genome shotgun (WGS) contigs from WGS project AACG00000000.2 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AACG00000000 was submitted to GenBank/EMBL/DDBJ by the Washington University School of Medicine.

When the Saccharomyces bayanus 623-6C map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., 623-6C).

Saccharomyces castellii NRRL Y-12630 Shows the Saccharomyces castellii NRRL Y-12630 whole genome shotgun (WGS) contigs from WGS project AACF00000000.1 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AACF00000000 was submitted to GenBank/EMBL/DDBJ by the Washington University School of Medicine.

When the Saccharomyces castellii NRRL Y-12630 map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., NRRL Y-12630).

Saccharomyces cerevisiae YJM789 Shows the Saccharomyces cerevisiae YJM789 whole genome shotgun (WGS) contigs from WGS project AAFW00000000.2 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AAFW00000000 was submitted to GenBank/EMBL/DDBJ by Stanford University.

When the Saccharomyces cerevisiae YJM789 map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., YJM789).

Saccharomyces kluyveri NRRL Y-12651 Shows the Saccharomyces kluyveri NRRL Y-12651 whole genome shotgun (WGS) contigs from WGS project AACE00000000.2 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AACE00000000 was submitted to GenBank/EMBL/DDBJ by the Washington University School of Medicine.

When the Saccharomyces kluyveri NRRL Y-12651 map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., NRRL Y-12651).

Saccharomyces kudriavzevii IFO 1802 Shows the Saccharomyces kudriavzevii IFO 1802 whole genome shotgun (WGS) contigs from WGS project AACI00000000.2 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AACI00000000 was submitted to GenBank/EMBL/DDBJ by the Washington University School of Medicine.

When the Saccharomyces kudriavzevii IFO 1802 map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., IFO 1802).

Saccharomyces mikatae IFO 1815 (Broad) Shows the Saccharomyces mikatae IFO 1815 (Broad) whole genome shotgun (WGS) contigs from WGS project AABZ00000000.1 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AABZ00000000 was submitted to GenBank/EMBL/DDBJ by the Broad Institute.

When the Saccharomyces mikatae IFO 1815 (Broad) map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., IFO 1815).

Saccharomyces mikatae IFO 1815 (WashU) Shows the Saccharomyces mikatae IFO 1815 (WashU) whole genome shotgun (WGS) contigs from WGS project AACH00000000.1 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AACH00000000 was submitted to GenBank/EMBL/DDBJ by the Washington University School of Medicine.

When the Saccharomyces mikatae IFO 1815 (WashU) map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., IFO 1815).

Saccharomyces paradoxus NRRL Y-17217 Shows the Saccharomyces paradoxus NRRL Y-17217 whole genome shotgun (WGS) contigs from WGS project AABY00000000.1 aligned to the assembled Saccharomyces cerevisiae S288c chromosomes. WGS project AABY00000000 was submitted to GenBank/EMBL/DDBJ by the Broad Institute.

When the Saccharomyces paradoxus NRRL Y-17217 map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the WGS contig and the chromosome to which it has been aligned; Total Bases, which shows the total number of bases in the WGS contig record; Aligned Bases, which shows the total number of bases from the WGS contig that aligned to the chromosome; % identity for the alignment; % coverage, which shows how much of the WGS contig aligned to the chromosome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the chromosome to the alignment length in the WGS contig; and Strain from which the WGS contig was derived (i.e., NRRL Y-17217).

Constructing queries back to top

Searchable Terms back to top

The Saccharomyces cerevisiae data are searchable with the following types of terms:

  • accessions
    e.g., NC_001144 or AABY01000679
  • gene symbols/systematic names/locus-tags
    e.g., a search for the symbol MRPL49 will retrieve the locus named Mitochondrial ribosomal protein of the large subunit.
    Sometimes two or more symbols refer to the same locus and are therefore considered synonyms or aliases. In these cases, any one of the terms will retrieve the locus.
  • marker names
    e.g., MAK27
  • clone names
    e.g., "ATCC:70840" or "WashU:7202"
  • text words
    e.g., a search for kinase will retrieve all map objects containing that word in their description.
    If multiple terms are entered, they will automatically be combined with the 'AND' Boolean operator.

Map Positions back to top

As noted in the Search By Position section of the general Map Viewer Help document, there are three main ways to search by map position from the Map View of a chromosome:
  1. Enter a range of interest in the Region text boxes in the left sidebar.
  2. Click on the region of interest in the chromosome thumbnail graphic in the sidebar.
  3. Click on a region of interest in the enlarged Map View of the chromosome.

For Saccharomyces cerevisiae, the following types of terms can be entered as map positions in the left sidebar text boxes noted in option 1:

  • symbols/marker/accessions - you can enter gene symbols/systematic names/locus-tags, markers, or accessions to display a region of the chromosome between those mapped elements. Note that both mapped elements must be present on maps that share the same coordinate system as the master map in order for the range search to work properly.
  • numerical positions - can be used if the master map is a sequence map or a genetic map. It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map (i.e., basepairs for the sequence maps and centiMorgans for the genetic map). Note that for a sequence map, basepair positions may be entered in any of the following formats: 1000000 or 1,000,000 or 1000K or 1M.

It is not necessary to enter a value in both Region text boxes. If you enter a value only in the upper box, the Map Viewer will display the region of the chromosome starting from that point and ending at the lower end of the chromosome. If you enter a value only in the lower box, the Map Viewer will display the region of the chromosome starting at the upper end of the chromosome and ending at the value entered.

General Tips back to top

As mentioned in the Searchable Terms section of the Map Viewer Help Document, any term entered in the query box will be treated as an independent entity to be joined by the 'AND' Boolean operator. It is also possible to construct more complex queries by using explicit Boolean operators (AND, OR, NOT) and field restrictions, and by limiting retrieval to records that have certain properties.

The Advanced Search page allows you to use a number of query options by simply checking boxes or radio buttons that represent various search fields, properties, and object types. It also allows you to limit your query to one or more chromosomes. The Advanced Search page is accessible from the header region of the genome view page.

Constructing URLs that link to Map Viewer back to top

If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region. For example:

Questions or Comments?
Write to the NCBI Service Desk