This directory contains the Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) assembly of the chicken genome
(galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2)), as well as repeat annotations and GenBank sequences.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/111
http://www.ncbi.nlm.nih.gov/genome/assembly/317958
http://www.ncbi.nlm.nih.gov/bioproject/13342
Files included in this directory:
galGal4.2bit - contains the complete chicken/galGal4 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
galGal4.agp.gz - Description of how the assembly was generated from
fragments.
galGal4.fa.gz - "Soft-masked" assembly sequence in one file.
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.
galGal4.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
galGal4.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. April 26 2011 (open-3-3-0) version of RepeatMasker,
RepeatMaskerLib.embl version: CC RELEASE 20110920
galGal4.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
est.fa.gz - Chicken ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
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 of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might be slightly out of sync with
the RefSeq data which is updated daily for most assemblies.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - 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.
galGal4.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
galGal4.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
galGal4.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
galGal4.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
galGal4.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/galGal4/bigZips. 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/galGal4/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
------------------------------------------------------------------
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.
------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
est.fa.gz 2019-10-17 04:43 142M
est.fa.gz.md5 2019-10-17 04:43 44
galGal4.2bit 2012-01-05 10:17 296M
galGal4.agp.gz 2012-05-25 14:53 238K
galGal4.chrom.sizes 2012-01-04 14:35 379K
galGal4.chromAlias.bb 2022-09-08 14:12 5.0M
galGal4.chromAlias.txt 2022-09-08 14:12 1.0M
galGal4.fa.gz 2012-05-25 15:01 330M
galGal4.fa.masked.gz 2012-05-25 15:07 273M
galGal4.fa.out.gz 2012-05-25 14:53 16M
galGal4.gc5Base.wib 2019-01-17 14:47 198M
galGal4.gc5Base.wig.gz 2019-01-17 14:47 4.2M
galGal4.gc5Base.wigVarStep.gz 2012-01-04 14:40 522M
galGal4.trf.bed.gz 2012-05-25 14:53 1.5M
genes/ 2020-02-05 13:47 -
md5sum.txt 2019-01-17 15:54 638
mrna.fa.gz 2019-10-17 04:27 12M
mrna.fa.gz.md5 2019-10-17 04:27 45
refMrna.fa.gz 2019-10-17 04:44 5.3M
refMrna.fa.gz.md5 2019-10-17 04:44 48
upstream1000.fa.gz 2012-05-25 15:10 1.2M
upstream2000.fa.gz 2012-05-25 15:11 2.4M
upstream5000.fa.gz 2012-05-25 15:11 5.7M
xenoMrna.fa.gz 2019-10-17 04:37 6.8G
xenoMrna.fa.gz.md5 2019-10-17 04:37 49
xenoRefMrna.fa.gz 2019-10-17 04:44 326M
xenoRefMrna.fa.gz.md5 2019-10-17 04:44 52