This directory contains download files of the Saccharomyces cerevisiae genome sequence and associated annotations. The data is based on sequence dated April 2011 in the Saccharomyces Genome Database (http://www.yeastgenome.org/) and was obtained from the site ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/fungi/Saccharomyces_cerevisiae/SacCer_Apr2011/ The S288C strain was used in this sequencing project. Files included in this directory: sacCer3.2bit - contains the complete S. cerevisiae/sacCer3 genome sequence in the 2bit file format. No masking has been applied to these sequences. The utility program, twoBitToFa (available from the kent src tree), can be used to extract .fa file(s) from this file. A pre-compiled version of the command line tool can be found at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ See also: http://genome.ucsc.edu/admin/git.html http://genome.ucsc.edu/admin/jk-install.html chromAgp.tar.gz - contains the list of accession identifiers for each chromosome, unpacking to one file per chromosome. chromFa.tar.gz - The assembly sequence in one file per chromosome. No masking has been applied to these sequences. There are NO RepeatMasker .out files for this assembly. chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED 5+ format (one file per chromosome). est.fa.gz - S. cerevisiae ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - checksums of files in this directory mrna.fa.gz - S. cerevisiae mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. sacCer3.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. sacCer3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track sacCer3.gc5Base.wig.gz - wiggle database table for the GC Percent track - this is an older standard alternative to the current - bigWig format of the track, sometimes usefull for analysis sacCer3.gc5Base.wib - binary data to correspond with the gc5Base.wig file see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database for a discussion of how to use the wig.gz and .wib files for interaction with the GC percent data values sacCer3.chromAlias.txt - sequence name alias file, one line for each sequence name. First column is sequence name followed by tab separated alias names. ------------------------------------------------------------------ If you plan to download a large file or multiple files from this directory, we recommend that you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu [username: anonymous, password: your email address], then cd to the directory goldenPath/sacCer3/bigZips. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) Alternate methods to ftp access. Using an rsync command to download the entire directory: rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf .tar.gz To uncompress the fa.gz files: gunzip .fa.gz --------------------------------------------------------------------- All the tables in this directory are freely available for public use. ---------------------------------------------------------------------