This directory contains the May 2006 assembly of the chicken genome
(galGal3, Chicken Genome Sequencing Consortium May 2006 release), 
as well as repeat annotations and GenBank sequences.

This assembly was produced by the Genome Sequencing Center at the 
Washington University School of Medicine in St. Louis.
For more information on the chicken genome, see the project website:
  http://genome.wustl.edu/genome.cgi?GENOME=Gallus%20gallus

Files included in this directory:

galGal3.2bit - contains the complete chicken/galGal3 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.
    The March 20 2006 (open-3-1-5) version of RepeatMasker and the 
    library release 20060315 were used.

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).

est.fa.gz - Chicken ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

galGal3.quals.fa.gz - quality scores in fasta file format

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Chicken mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
    This sequence data is updated once a week via automatic GenBank
    updates.

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts for RefSeq genes with annotated 5' UTRs.  
    This file is updated weekly so it could be slightly out      
    of sync with the RefSeq data which is updated daily for most
    assemblies.

upstream2000.zip - Same as upstream1000, but 2000 bases.

upstream5000.zip - Same as upstream1000, but 5000 bases.

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.

galGal3.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 hgdownload.cse.ucsc.edu, then 
go to the directory goldenPath/galGal3/bigZips. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

The Chicken sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
   if the providers of these data are properly cited:
   International Chicken Genome Sequencing Consortium.  
   Sequence and comparative analysis of the chicken genome provide unique
   perspectives on vertebrate evolution.
   Nature. 2004 Dec 9;432(7018):695-716.  PMID: 15592404
   See http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. Any redistribution of the data should carry this notice.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 4.3K 
[   ]chromAgp.tar.gz04-Aug-2006 15:35 2.0M 
[   ]chromFa.tar.gz04-Aug-2006 15:40 318M 
[   ]chromFaMasked.tar.gz04-Aug-2006 15:44 283M 
[   ]chromOut.tar.gz04-Aug-2006 15:35 15M 
[   ]chromTrf.tar.gz04-Aug-2006 15:44 1.3M 
[   ]galGal3.2bit15-May-2006 08:55 267M 
[   ]galGal3.chrom.sizes15-May-2006 17:24 947  
[   ]galGal3.quals.fa.gz09-Jun-2009 10:39 125M 
[TXT]md5sum.txt10-Dec-2013 12:02 355  
[   ]upstream1000.fa.gz04-Aug-2006 15:50 895K 
[   ]upstream2000.fa.gz04-Aug-2006 15:50 1.7M 
[   ]upstream5000.fa.gz04-Aug-2006 15:50 4.2M 

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