SGD Help: Reference Sequence


Welcome to this quick tutorial on describing
different ways to find information about the yeast reference genome at SGD. The Saccharomyces cerevisiae reference genome
sequence is from strain S288C. You can find details about S288C on the SGD
Strain page for S288C. This page can be found by searching “S288C”, then, by clicking on Strain names on the left
hand side, and then on S288C. From the Strain page, you can access GenBank
and RefSeq files for the 16 nuclear chromosomes and mitochondria for the S288C reference genome. You can also find an overview section giving
the genotype and the description of the strain. The GenBank and RefSeq accession IDs and assembly
statistics can be found in the Genome section shown here. From the S288C strain page, you can access
individual chromosome pages. These pages contain current annotation details
from each chromosome. Click on any chromosome and it will direct
you to the page showing an overview and features section. You can download the chromosome sequence in
FASTA format by clicking on the Download sequence button. The chromosome pages can also be accessed
from the locus summary pages and the gene sequence tab pages. From the chromosome pages you can also go
to NCBI, or back to the S288C strain page. Complete summaries of sequence and/or annotation
updates made for each chromosome since the initial genome release of July 31st, 1996
are available via chromosome history pages. These pages can be found by clicking on the
sequence dropdown menu on the homepage and scrolling down to the reference genome and
then chromosome history. On this page, you can find chromosome histories
for individual chromosomes by clicking on these links, taking you to a new page for
that specific chromosome. The release dates of all S. cerevisiae S288C
genome releases are listed in the “dates of genome releases” tab file on SGD’s download
site. To find the download site, click on the Sequence
dropdown menu and select Download. Scroll down to the “dates_of_genome_releases.tab”
and click to show the list of dates. Compressed data files for current and archived
genome releases can be found on SGD’s download site. You can access them by clicking on this link. Lastly, the original genome sequence released
in 1996 is described in the Systematic Sequencing Table. This page can be accessed from the homepage
by clicking on Sequence and scrolling down to Reference Genome and Systematic Sequencing
Table. On this page, you can find chromosome statistics
and retrieval options. If you have any further questions, please
contact us here at [email protected]lists.stanford.edu

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