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.
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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/oviAri1/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/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 <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
Name Last modified Size Description
Parent Directory -
genes/ 2020-02-05 13:47 -
est.fa.gz.md5 2019-10-17 15:27 44
mrna.fa.gz.md5 2019-10-17 15:22 45
refMrna.fa.gz.md5 2019-10-17 15:28 48
xenoMrna.fa.gz.md5 2016-03-16 14:49 49
xenoRefMrna.fa.gz.md5 2019-10-17 15:28 52
upstream1000.fa.gz.md5 2019-10-17 15:28 53
upstream2000.fa.gz.md5 2019-10-17 15:28 53
upstream5000.fa.gz.md5 2019-10-17 15:29 53
md5sum.txt 2012-04-02 09:22 304
oviAri1.chrom.sizes 2010-04-14 15:55 25K
upstream1000.fa.gz 2019-10-17 15:28 78K
upstream2000.fa.gz 2019-10-17 15:28 139K
upstream5000.fa.gz 2019-10-17 15:29 301K
refMrna.fa.gz 2019-10-17 15:28 458K
oviAri1.trf.bed.gz 2011-02-07 09:41 501K
mrna.fa.gz 2019-10-17 15:22 966K
oviAri1.agp.gz 2011-02-07 09:40 60M
oviAri1.fa.out.gz 2011-02-07 09:41 61M
est.fa.gz 2019-10-17 15:27 65M
xenoRefMrna.fa.gz 2019-10-17 15:28 330M
oviAri1.fa.masked.gz 2011-02-07 09:53 337M
oviAri1.fa.gz 2011-02-07 09:47 426M
oviAri1.2bit 2010-04-14 19:15 718M
xenoMrna.fa.gz 2016-03-16 14:49 5.0G