This directory contains the Oct. 2007 assembly of the cow genome (bosTau4, Baylor Release 4.0), as well as repeat annotations and GenBank sequences. This assembly was produced by the Baylor College of Medicine Human Genome Sequencing Center. For more information on the cow genome, see the Baylor College of Medicine Human Genome Sequencing Center project website at http://www.hgsc.bcm.tmc.edu/projects/bovine/ Files included in this directory: bosTau4.2bit - contains the complete cow/bosTau4 genome sequence in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. 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 bosTau4.agp.gz - Description of how the assembly was generated from fragments. bosTau4.fa.gz - "Soft-masked" assembly sequence in one file. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. bosTau4.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. bosTau4.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. # Jan 11 2008 (open-3-1-9) version of RepeatMasker # CC RELEASE 20071204; bosTau4.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED format. est.fa.gz - Cow ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. bosTau4.quals.fa.gz - quality scores in fasta file format md5sum.txt - checksums of files in this directory mrna.fa.gz - Cow mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for MGC Genes with annotated 5' UTRs. This file is updated weekly so it could be slightly out of synch with the MGC Gene data which is updated daily for most assemblies. upstream2000.fa.gz - Same as upstream1000, but 2000 bases. upstream5000.fa.gz - Same as upstream1000, but 5000 bases. xenoMrna.fa.gz - GenBank mRNAs from species other than that of the genome. This sequence data is updated once a week via automatic GenBank updates. bosTau4.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ------------------------------------------------------------------ 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/bosTau4/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/bosTau4/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/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 For conditions of use regarding the Cow genome sequence data, see http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html .
Name Last modified Size Description
Parent Directory - bosTau4.2bit 2008-03-10 11:27 729M bosTau4.agp.gz 2008-03-19 15:38 2.9M bosTau4.chrom.sizes 2008-03-07 15:55 238K bosTau4.fa.gz 2008-03-19 15:53 857M bosTau4.fa.masked.gz 2008-03-19 16:02 483M bosTau4.fa.out.gz 2008-03-19 15:39 161M bosTau4.quals.fa.gz 2009-06-09 10:30 354M bosTau4.trf.bed.gz 2008-03-19 15:40 2.6M est.fa.gz 2020-02-27 17:46 314M est.fa.gz.md5 2020-02-27 17:46 44 genes/ 2020-02-05 13:46 - md5sum.txt 2014-01-03 14:54 358 mrna.fa.gz 2020-02-27 17:39 11M mrna.fa.gz.md5 2020-02-27 17:39 45 refMrna.fa.gz 2020-02-27 17:46 11M refMrna.fa.gz.md5 2020-02-27 17:46 48 upstream1000.fa.gz 2020-02-27 17:47 2.8M upstream1000.fa.gz.md5 2020-02-27 17:47 53 upstream2000.fa.gz 2020-02-27 17:47 5.3M upstream2000.fa.gz.md5 2020-02-27 17:47 53 upstream5000.fa.gz 2020-02-27 17:47 13M upstream5000.fa.gz.md5 2020-02-27 17:47 53 xenoMrna.fa.gz 2016-03-22 13:14 5.0G xenoMrna.fa.gz.md5 2016-03-22 13:14 49 xenoRefMrna.fa.gz 2020-02-27 17:46 326M xenoRefMrna.fa.gz.md5 2020-02-27 17:46 52