This directory contains the Btau_2.0 cow genome assembly (bosTau2, Mar. 2005) produced by the Baylor College of Medicine Human Genome Sequencing Center. For more information about these data, see the Baylor web page at http://www.hgsc.bcm.tmc.edu/projects/bovine/. Files in this directory include: bosTau2.2bit - contains the complete cow/bosTau2 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 bosTau2.hardmask.fa.gz Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown as Ns; non-repeating sequence is shown in upper case. bosTau2.softmask.fa.gz Repeats from RepeatMasker are shown in lower case; non-repeating sequence is shown in upper case. bosTau2.softmask2.fa.gz 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. RepeatMasker July 2004 version with RepBase libraries: RepBase Update 9.04, RM database version 20040702. est.fa.gz - Cow ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - MD5 checksum of these files to verify correct transmission. mrna.fa.gz - Cow mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. UCSC_Cow2.0.agp.gz - Description of how the assembly was generated from fragments. Downloaded from Baylor Jul. 18, 2005. UCSC_Cow2.0.fa.gz - Sequences downloaded from Baylor Jul. 18, 2005. UCSC modifications made to the original data set: - Chr changed to chr - Chr30 renamed to chrX - ChrUn split into scaffold1 through scaffold98058 - Bin0 fragments assembled into artificial chromosome chrBin0 with 500 bp-gap padding - chrM obtained from NCBI (gi=12800) bosTau2.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 you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/bosTau2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) Please review the restrictions on the use of the cow assembly data at http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html.
Name Last modified Size Description
Parent Directory - UCSC_Cow2.0.agp.gz 2005-07-23 16:27 15M UCSC_Cow2.0.fa.gz 2005-07-23 16:29 838M bosTau2.2bit 2005-07-26 13:38 883M bosTau2.chrom.sizes 2005-07-23 15:45 1.7M bosTau2.fa.gz 2020-01-23 02:19 892M bosTau2.hardmask.fa.gz 2005-07-26 13:33 513M bosTau2.softmask.fa.gz 2005-07-26 13:28 892M bosTau2.softmask2.fa.gz 2005-07-26 13:30 892M est.fa.gz 2019-10-16 19:38 314M est.fa.gz.md5 2019-10-16 19:38 44 md5sum.txt 2014-02-03 10:20 324 mrna.fa.gz 2019-10-16 19:31 11M mrna.fa.gz.md5 2019-10-16 19:31 45 refMrna.fa.gz 2019-10-16 19:38 11M refMrna.fa.gz.md5 2019-10-16 19:38 48 upstream1000.fa.gz 2019-10-16 19:39 3.0M upstream1000.fa.gz.md5 2019-10-16 19:39 53 upstream2000.fa.gz 2019-10-16 19:40 5.7M upstream2000.fa.gz.md5 2019-10-16 19:40 53 upstream5000.fa.gz 2019-10-16 19:41 13M upstream5000.fa.gz.md5 2019-10-16 19:41 53 xenoRefMrna.fa.gz 2019-10-16 19:38 320M xenoRefMrna.fa.gz.md5 2019-10-16 19:38 52