This directory contains the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly of the sheep genome (oviAri1, ISGC (NCBI project 10709, accession GCA_000005525.1)), as well as repeat annotations and GenBank sequences. This assembly was produced by the International Sheep Genomics Consortium (ISGC). For more information on the sheep genome, see the project website: http://www.sheephapmap.org/ http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33937 Files included in this directory: oviAri1.2bit - contains the complete sheep/oviAri1 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 oviAri1.agp.gz - Description of how the assembly was generated from fragments. oviAri1.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. oviAri1.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. oviAri1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. June 4 2009 (open-3-2-8) version of RepeatMasker RepeatMaskerLib.embl version: 20090604; oviAri1.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 - Sheep 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 - Sheep mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. 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. oviAri1.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/oviAri1/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/oviAri1/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/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