This directory contains the Oct. 2010 (CGSC 2.1.3/panTro3) assembly of
the chimp genome (panTro3, CGSC 2.1.3 (GCA_000001515.3)), as well as
repeat annotations and GenBank sequences.
This assembly was produced by Chimpanzee Sequencing and Analysis Consortium.
For more information on the chimp genome, see the project website:
http://genome.wustl.edu/genomes/view/pan_troglodytes/
Files included in this directory:
panTro3.2bit - contains the complete chimp/panTro3 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
panTro3.agp.gz - Description of how the assembly was generated from
fragments.
panTro3.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.
panTro3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
panTro3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RepeatMasker version: June 30 2010 (open-3-2-9)
RepeatMasker library version: 20090604
panTro3.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.
md5sum.txt - checksums of files in this directory
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.
panTro3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
panTro3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
panTro3.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
panTro3.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
panTro3.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/panTro3/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/panTro3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/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 chimpanzee sequence is made freely available before scientific
publication 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
particular genes and regions if the providers of these data are
properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html
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 (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
est.fa.gz 2019-10-17 16:29 2.7M
est.fa.gz.md5 2019-10-17 16:29 44
genes/ 2020-02-05 13:47 -
md5sum.txt 2019-01-17 15:57 479
mrna.fa.gz 2019-10-17 16:14 1.9M
mrna.fa.gz.md5 2019-10-17 16:14 45
panTro3.2bit 2011-02-22 09:30 822M
panTro3.agp.gz 2011-02-23 13:11 4.4M
panTro3.chrom.sizes 2011-02-17 14:20 654K
panTro3.chromAlias.bb 2022-09-08 14:14 5.8M
panTro3.chromAlias.txt 2022-09-08 14:14 886K
panTro3.fa.gz 2011-02-23 13:27 905M
panTro3.fa.masked.gz 2011-02-23 13:36 479M
panTro3.fa.out.gz 2011-02-23 13:13 163M
panTro3.gc5Base.wib 2019-01-17 14:52 566M
panTro3.gc5Base.wig.gz 2019-01-17 14:52 12M
panTro3.gc5Base.wigVarStep.gz 2011-02-17 14:29 1.4G
panTro3.trf.bed.gz 2011-02-23 13:13 7.3M
refMrna.fa.gz 2019-10-17 16:29 1.5M
refMrna.fa.gz.md5 2019-10-17 16:29 48
upstream1000.fa.gz 2019-10-17 16:30 3.9M
upstream1000.fa.gz.md5 2019-10-17 16:30 53
upstream2000.fa.gz 2019-10-17 16:31 7.4M
upstream2000.fa.gz.md5 2019-10-17 16:31 53
upstream5000.fa.gz 2019-10-17 16:31 18M
upstream5000.fa.gz.md5 2019-10-17 16:31 53
xenoMrna.fa.gz 2019-10-17 16:25 6.8G
xenoMrna.fa.gz.md5 2019-10-17 16:25 49
xenoRefMrna.fa.gz 2019-10-17 16:29 329M
xenoRefMrna.fa.gz.md5 2019-10-17 16:29 52