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
chr11.fa.gz 2008-08-06 15:25 6.7M
chr12.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
chr24.fa.gz 2008-08-06 15:25 2.4M
chr23.fa.gz 2008-08-06 15:25 1.9M
chr21.fa.gz 2008-08-06 15:25 1.8M
chr8_random.fa.gz 2008-08-06 15:25 1.6M
chr4_random.fa.gz 2008-08-06 15:25 1.6M
chr28.fa.gz 2008-08-06 15:25 1.5M
chr26.fa.gz 2008-08-06 15:25 1.5M
chr27.fa.gz 2008-08-06 15:25 1.4M
chr22.fa.gz 2008-08-06 15:25 1.0M
chrZ_random.fa.gz 2008-08-06 15:25 944K
chr13_random.fa.gz 2008-08-06 15:25 822K
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
chr2_random.fa.gz 2008-08-06 15:25 571K
chr26_random.fa.gz 2008-08-06 15:25 489K
chr3_random.fa.gz 2008-08-06 15:25 413K
chr25.fa.gz 2008-08-06 15:25 387K
chr1_random.fa.gz 2008-08-06 15:25 381K
chr1B.fa.gz 2008-08-06 15:25 325K
chrLGE22.fa.gz 2008-08-06 15:25 274K
chr22_random.fa.gz 2008-08-06 15:25 233K
chr1A_random.fa.gz 2008-08-06 15:25 213K
chr7_random.fa.gz 2008-08-06 15:25 188K
chr10_random.fa.gz 2008-08-06 15:25 174K
chr23_random.fa.gz 2008-08-06 15:25 163K
chr18_random.fa.gz 2008-08-06 15:25 147K
chr25_random.fa.gz 2008-08-06 15:25 140K
chrLGE22_random.fa.gz 2008-08-06 15:25 134K
chr9_random.fa.gz 2008-08-06 15:25 117K
chr15_random.fa.gz 2008-08-06 15:25 112K
chr12_random.fa.gz 2008-08-06 15:25 110K
chr11_random.fa.gz 2008-08-06 15:25 94K
chr20_random.fa.gz 2008-08-06 15:25 92K
chr4A_random.fa.gz 2008-08-06 15:25 83K
chr14_random.fa.gz 2008-08-06 15:25 78K
chr17_random.fa.gz 2008-08-06 15:25 66K
chr19_random.fa.gz 2008-08-06 15:25 64K
chr27_random.fa.gz 2008-08-06 15:25 64K
chr28_random.fa.gz 2008-08-06 15:25 61K
chr24_random.fa.gz 2008-08-06 15:25 58K
chr16_random.fa.gz 2008-08-06 15:25 49K
chr1B_random.fa.gz 2008-08-06 15:25 42K
chrLG2.fa.gz 2008-08-06 15:25 31K
chrM.fa.gz 2008-08-06 15:25 5.5K
chrLG5.fa.gz 2008-08-06 15:25 4.3K
md5sum.txt 2008-08-06 15:44 3.4K
chr16.fa.gz 2008-08-06 15:25 2.4K