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:

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:
    See also:

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.

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, 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)

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
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 - chromAgp.tar.gz 2007-02-15 11:43 1.2M chromFa.tar.gz 2007-02-15 11:55 765M chromFaMasked.tar.gz 2007-02-15 12:03 466M chromOut.tar.gz 2007-02-15 11:43 113M chromTrf.tar.gz 2007-02-15 12:03 1.6M equCab1.2bit 2007-02-15 11:32 612M equCab1.chrom.sizes 2007-02-12 13:30 500 equCab1.fa.gz 2020-01-23 02:21 766M equCab1.quals.fa.gz 2009-06-09 10:29 195M est.fa.gz 2019-10-17 02:54 7.1M est.fa.gz.md5 2019-10-17 02:54 44 genes/ 2020-02-05 13:47 - md5sum.txt 2014-01-03 16:13 355 mrna.fa.gz 2019-10-17 02:40 7.6M mrna.fa.gz.md5 2019-10-17 02:40 45 refMrna.fa.gz 2019-10-17 02:55 883K refMrna.fa.gz.md5 2019-10-17 02:55 48 upstream1000.fa.gz 2019-10-17 02:55 236K upstream1000.fa.gz.md5 2019-10-17 02:55 53 upstream2000.fa.gz 2019-10-17 02:55 453K upstream2000.fa.gz.md5 2019-10-17 02:55 53 upstream5000.fa.gz 2019-10-17 02:55 1.1M upstream5000.fa.gz.md5 2019-10-17 02:55 53 xenoMrna.fa.gz 2019-10-17 02:50 6.8G xenoMrna.fa.gz.md5 2019-10-17 02:50 49 xenoRefMrna.fa.gz 2019-10-17 02:55 330M xenoRefMrna.fa.gz.md5 2019-10-17 02:55 52