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.

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

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