This directory contains download files of the Saccharomyces
cerevisiae genome sequence and associated annotations. The data
is based on sequence dated June 2008 in the Saccharomyces Genome
Database (http://www.yeastgenome.org/) and was obtained from the site
http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/
The S288C strain was used in this sequencing project.

Files included in this directory:

sacCer2.2bit - contains the complete genome sequence in the 2bit file format.
    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
    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.

sgdGene.upstream*.fa.gz - Saccharomyces Genome Database genes upstream
	sequences, 1000, 2000 and 5000 bases


sacCer2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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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/sacCer2/bigZips. To download multiple files, use
the "mget" command:

    mget <filename1> <filename2> ...
    - 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/sacCer2/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz


All the tables in this directory are freely available for public use.