This directory contains the Sep. 2007 assembly of the horse genome
(equCab2, Broad Institute EquCab2) in one gzip-compressed FASTA file per
chromosome.
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:
- chr*.fa.gz: compressed FASTA sequence of each 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.
RepeatMasker was run with the -s (sensitive) setting.
Jan 11 2008 (open-3-1-9) version of RepeatMasker, RELEASE 20071204.
- md5sum.txt: checksums of files in this directory
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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/equCab2/chromosomes. 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/equCab2/chromosomes/ .
For a single file, e.g. chrM.fa.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/equCab2/chromosomes/chrM.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/equCab2/chromosomes/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/equCab2/chromosomes/chrM.fa.gz'
-O chrM.fa.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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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 provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves 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 -
chr1.fa.gz 2008-09-09 12:29 58M
chrX.fa.gz 2008-09-09 12:29 39M
chr2.fa.gz 2008-09-09 12:30 38M
chr3.fa.gz 2008-09-09 12:30 38M
chr4.fa.gz 2008-09-09 12:30 34M
chr5.fa.gz 2008-09-09 12:30 31M
chr7.fa.gz 2008-09-09 12:30 31M
chr8.fa.gz 2008-09-09 12:31 30M
chr14.fa.gz 2008-09-09 12:31 30M
chr15.fa.gz 2008-09-09 12:31 29M
chr16.fa.gz 2008-09-09 12:31 28M
chr6.fa.gz 2008-09-09 12:31 27M
chr9.fa.gz 2008-09-09 12:31 26M
chr10.fa.gz 2008-09-09 12:31 26M
chr18.fa.gz 2008-09-09 12:32 26M
chr17.fa.gz 2008-09-09 12:32 25M
chrUn.fa.gz 2008-09-09 12:30 25M
chr20.fa.gz 2008-09-09 12:32 20M
chr11.fa.gz 2008-09-09 12:32 19M
chr19.fa.gz 2008-09-09 12:32 19M
chr21.fa.gz 2008-09-09 12:32 18M
chr23.fa.gz 2008-09-09 12:32 18M
chr22.fa.gz 2008-09-09 12:32 16M
chr24.fa.gz 2008-09-09 12:32 15M
chr28.fa.gz 2008-09-09 12:32 14M
chr13.fa.gz 2008-09-09 12:32 13M
chr26.fa.gz 2008-09-09 12:33 13M
chr27.fa.gz 2008-09-09 12:32 13M
chr25.fa.gz 2008-09-09 12:33 12M
chr29.fa.gz 2008-09-09 12:33 11M
chr12.fa.gz 2008-09-09 12:33 10M
chr30.fa.gz 2008-09-09 12:33 9.5M
chr31.fa.gz 2008-09-09 12:33 7.9M
chrM.fa.gz 2008-09-09 12:33 5.4K
md5sum.txt 2008-09-09 13:14 1.5K