This directory contains the Jan. 2007 assembly of the horse genome
(equCab1, Broad Institute equCab1 1.0), as well as repeat annotations and
GenBank sequences.
This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the horse genome, see the project website:
http://www.broad.mit.edu/mammals/horse/.
Files included in this directory:
equCab1.2bit - contains the complete horse/equCab1 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
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting using the
October 6 2006 (open-3-1-6) version of RepeatMasker, RELEASE 20061006.
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).
equCab1.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
equCab1.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, then
go to the directory goldenPath/equCab1/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
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The horse sequence is made freely available before scientific publication
from the Broad Institute with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions if the providers of this data (the Broad Institute) are
properly acknowledged.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification of
regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that is,
30 Mb or more).
4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
genes/ 2020-02-05 13:47 -
equCab1.fa.gz 2020-01-23 02:21 766M
upstream5000.fa.gz.md5 2019-10-17 02:55 53
upstream5000.fa.gz 2019-10-17 02:55 1.1M
upstream2000.fa.gz.md5 2019-10-17 02:55 53
upstream2000.fa.gz 2019-10-17 02:55 453K
upstream1000.fa.gz.md5 2019-10-17 02:55 53
upstream1000.fa.gz 2019-10-17 02:55 236K
refMrna.fa.gz.md5 2019-10-17 02:55 48
refMrna.fa.gz 2019-10-17 02:55 883K
xenoRefMrna.fa.gz.md5 2019-10-17 02:55 52
xenoRefMrna.fa.gz 2019-10-17 02:55 330M
est.fa.gz.md5 2019-10-17 02:54 44
est.fa.gz 2019-10-17 02:54 7.1M
xenoMrna.fa.gz.md5 2019-10-17 02:50 49
xenoMrna.fa.gz 2019-10-17 02:50 6.8G
mrna.fa.gz.md5 2019-10-17 02:40 45
mrna.fa.gz 2019-10-17 02:40 7.6M
md5sum.txt 2014-01-03 16:13 355
equCab1.quals.fa.gz 2009-06-09 10:29 195M
chromTrf.tar.gz 2007-02-15 12:03 1.6M
chromFaMasked.tar.gz 2007-02-15 12:03 466M
chromFa.tar.gz 2007-02-15 11:55 765M
chromOut.tar.gz 2007-02-15 11:43 113M
chromAgp.tar.gz 2007-02-15 11:43 1.2M
equCab1.2bit 2007-02-15 11:32 612M
equCab1.chrom.sizes 2007-02-12 13:30 500