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