This directory contains the Jul. 2008 assembly of the zebra finch genome
(taeGut1, WUSTL v3.2.4) in one gzip-compressed FASTA file per chromosome.

This assembly was produced by the Genome Sequencing Center at the Washington 
University in St. Louis (WUSTL) School of Medicine. For more information on 
the zebra finch genome, see the project website:
    http://genome.wustl.edu/genome.cgi?GENOME=Taeniopygia%20guttata

Files included in this directory:

  - chr*.fa.gz: compressed FASTA sequence of each chromosome.
    Repeats from WindowMasker are shown in lower case; non-repeating sequence
    is shown in upper case.

  - Checksum values for all files in this directory can be found in
    md5sum.txt.

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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/taeGut1/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/taeGut1/chromosomes/ .
For a single file, e.g. chrM.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/chromosomes/chrM.fa.gz .
    
Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/chromosomes/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/chromosomes/chrM.fa.gz' 
        -O chrM.fa.gz
    
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

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The Zebra finch 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 acknowledged.  See
   http://genome.wustl.edu/data.cgi for credit information.

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.

4. This is in accordance with, and with the understandings in the Fort
   Lauderdale meeting discussing Community Resource Projects (see
   http://www.wellcome.ac.uk/doc_wtd003208.html) and the resulting
   NHGRI policy statement (http://www.genome.gov/page.cfm?pageID=10506537).

5. Any redistribution of the data should carry this notice.

      Name                    Last modified      Size  Description
Parent Directory - chrUn.fa.gz 2008-08-06 15:23 54M chr2.fa.gz 2008-08-06 15:24 49M chr1.fa.gz 2008-08-06 15:24 37M chr3.fa.gz 2008-08-06 15:24 36M chr1A.fa.gz 2008-08-06 15:24 23M chrZ.fa.gz 2008-08-06 15:24 23M chr4.fa.gz 2008-08-06 15:24 22M chr5.fa.gz 2008-08-06 15:25 19M chr7.fa.gz 2008-08-06 15:25 12M chr6.fa.gz 2008-08-06 15:25 11M chr8.fa.gz 2008-08-06 15:25 8.7M chr9.fa.gz 2008-08-06 15:25 8.4M chr12.fa.gz 2008-08-06 15:25 6.7M chr11.fa.gz 2008-08-06 15:25 6.7M chr10.fa.gz 2008-08-06 15:25 6.4M chr4A.fa.gz 2008-08-06 15:25 6.4M chr13.fa.gz 2008-08-06 15:25 5.2M chr14.fa.gz 2008-08-06 15:25 5.1M chr20.fa.gz 2008-08-06 15:25 4.8M chr15.fa.gz 2008-08-06 15:25 4.4M chr17.fa.gz 2008-08-06 15:25 3.6M chr19.fa.gz 2008-08-06 15:25 3.6M chr18.fa.gz 2008-08-06 15:25 3.4M chr23.fa.gz 2008-08-06 15:25 1.9M chr24.fa.gz 2008-08-06 15:25 2.4M chr4_random.fa.gz 2008-08-06 15:25 1.6M chr21.fa.gz 2008-08-06 15:25 1.8M chr8_random.fa.gz 2008-08-06 15:25 1.6M chr26.fa.gz 2008-08-06 15:25 1.5M chr28.fa.gz 2008-08-06 15:25 1.5M chr13_random.fa.gz 2008-08-06 15:25 822K chr22.fa.gz 2008-08-06 15:25 1.0M chr27.fa.gz 2008-08-06 15:25 1.4M chrZ_random.fa.gz 2008-08-06 15:25 944K chr2_random.fa.gz 2008-08-06 15:25 571K chr3_random.fa.gz 2008-08-06 15:25 413K chr5_random.fa.gz 2008-08-06 15:25 780K chr6_random.fa.gz 2008-08-06 15:25 656K chr21_random.fa.gz 2008-08-06 15:25 573K chr26_random.fa.gz 2008-08-06 15:25 489K chr1A_random.fa.gz 2008-08-06 15:25 213K chr1B.fa.gz 2008-08-06 15:25 325K chr1_random.fa.gz 2008-08-06 15:25 381K chr7_random.fa.gz 2008-08-06 15:25 188K chr9_random.fa.gz 2008-08-06 15:25 117K chr10_random.fa.gz 2008-08-06 15:25 174K chr11_random.fa.gz 2008-08-06 15:25 94K chr12_random.fa.gz 2008-08-06 15:25 110K chr15_random.fa.gz 2008-08-06 15:25 112K chr18_random.fa.gz 2008-08-06 15:25 147K chr20_random.fa.gz 2008-08-06 15:25 92K chr22_random.fa.gz 2008-08-06 15:25 233K chr23_random.fa.gz 2008-08-06 15:25 163K chr25.fa.gz 2008-08-06 15:25 387K chr25_random.fa.gz 2008-08-06 15:25 140K chrLGE22.fa.gz 2008-08-06 15:25 274K chrLGE22_random.fa.gz 2008-08-06 15:25 134K chr1B_random.fa.gz 2008-08-06 15:25 42K chr4A_random.fa.gz 2008-08-06 15:25 83K chr14_random.fa.gz 2008-08-06 15:25 78K chr16.fa.gz 2008-08-06 15:25 2.4K chr16_random.fa.gz 2008-08-06 15:25 49K chr17_random.fa.gz 2008-08-06 15:25 66K chr19_random.fa.gz 2008-08-06 15:25 64K chr24_random.fa.gz 2008-08-06 15:25 58K chr27_random.fa.gz 2008-08-06 15:25 64K chr28_random.fa.gz 2008-08-06 15:25 61K chrLG2.fa.gz 2008-08-06 15:25 31K chrLG5.fa.gz 2008-08-06 15:25 4.3K chrM.fa.gz 2008-08-06 15:25 5.5K md5sum.txt 2008-08-06 15:44 3.4K