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
------------------------------------------------------------------
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

------------------------------------------------------------------
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. 

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt06-Apr-2010 12:24 2.8K 
[   ]chr1.fa.gz09-Sep-2008 12:29 58M 
[   ]chr2.fa.gz09-Sep-2008 12:30 38M 
[   ]chr3.fa.gz09-Sep-2008 12:30 38M 
[   ]chr4.fa.gz09-Sep-2008 12:30 34M 
[   ]chr5.fa.gz09-Sep-2008 12:30 31M 
[   ]chr6.fa.gz09-Sep-2008 12:31 27M 
[   ]chr7.fa.gz09-Sep-2008 12:30 31M 
[   ]chr8.fa.gz09-Sep-2008 12:31 30M 
[   ]chr9.fa.gz09-Sep-2008 12:31 26M 
[   ]chr10.fa.gz09-Sep-2008 12:31 26M 
[   ]chr11.fa.gz09-Sep-2008 12:32 19M 
[   ]chr12.fa.gz09-Sep-2008 12:33 10M 
[   ]chr13.fa.gz09-Sep-2008 12:32 13M 
[   ]chr14.fa.gz09-Sep-2008 12:31 30M 
[   ]chr15.fa.gz09-Sep-2008 12:31 29M 
[   ]chr16.fa.gz09-Sep-2008 12:31 28M 
[   ]chr17.fa.gz09-Sep-2008 12:32 25M 
[   ]chr18.fa.gz09-Sep-2008 12:32 26M 
[   ]chr19.fa.gz09-Sep-2008 12:32 19M 
[   ]chr20.fa.gz09-Sep-2008 12:32 20M 
[   ]chr21.fa.gz09-Sep-2008 12:32 18M 
[   ]chr22.fa.gz09-Sep-2008 12:32 16M 
[   ]chr23.fa.gz09-Sep-2008 12:32 18M 
[   ]chr24.fa.gz09-Sep-2008 12:32 15M 
[   ]chr25.fa.gz09-Sep-2008 12:33 12M 
[   ]chr26.fa.gz09-Sep-2008 12:33 13M 
[   ]chr27.fa.gz09-Sep-2008 12:32 13M 
[   ]chr28.fa.gz09-Sep-2008 12:32 14M 
[   ]chr29.fa.gz09-Sep-2008 12:33 11M 
[   ]chr30.fa.gz09-Sep-2008 12:33 9.5M 
[   ]chr31.fa.gz09-Sep-2008 12:33 7.9M 
[   ]chrM.fa.gz09-Sep-2008 12:33 5.4K 
[   ]chrUn.fa.gz09-Sep-2008 12:30 25M 
[   ]chrX.fa.gz09-Sep-2008 12:29 39M 
[TXT]md5sum.txt09-Sep-2008 13:14 1.5K 

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