This directory contains the Jul. 2007 assembly of the orangutan genome
(ponAbe2, WUSTL Pongo_albelii-2.0.2), as well as repeat annotations and
GenBank sequences.
This assembly was produced by the Genome Sequencing Center at the Washington
University School of Medicine in St. Louis, MO, USA.
For more information on the orangutan genome, see the project website:
http://genome.wustl.edu/genome.cgi?GENOME=Pongo%20abelii
Files included in this directory:
ponAbe2.2bit - contains the complete orangutan/ponAbe2 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
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
RepeatMasker version May 17 2007 (open-3-1-8)
library version RELEASE 20061006
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format (one file per chromosome).
ponAbe2.quality.fa.tar.gz - quality scores, individual fasta files for
each chrom.
Beware, this is 20Gb of data when unpacked and uncompressed
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Orangutan mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for Xeno RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the Xeno 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.
ponAbe2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
ponAbe2.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, then
go to the directory goldenPath/ponAbe2/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/ponAbe2/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/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 Orangutan 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.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 -
ponAbe2.chrom.sizes 2007-09-12 12:21 1.0K
ponAbe2.2bit 2007-09-19 14:31 858M
chromAgp.tar.gz 2007-10-01 17:33 10M
chromOut.tar.gz 2007-10-01 17:34 173M
chromFa.tar.gz 2007-10-01 17:49 960M
chromFaMasked.tar.gz 2007-10-01 17:57 506M
chromTrf.tar.gz 2007-10-01 17:57 7.6M
ponAbe2.quality.fa.tar.gz 2008-10-14 10:24 726M
ponAbe2.quals.fa.gz 2009-06-08 13:24 746M
md5sum.txt 2014-01-03 15:09 361
mrna.fa.gz 2019-10-17 18:02 4.6M
mrna.fa.gz.md5 2019-10-17 18:02 45
xenoMrna.fa.gz 2019-10-17 18:12 6.8G
xenoMrna.fa.gz.md5 2019-10-17 18:13 49
est.fa.gz 2019-10-17 18:17 8.9M
est.fa.gz.md5 2019-10-17 18:17 44
xenoRefMrna.fa.gz 2019-10-17 18:17 327M
xenoRefMrna.fa.gz.md5 2019-10-17 18:17 52
refMrna.fa.gz 2019-10-17 18:17 3.4M
refMrna.fa.gz.md5 2019-10-17 18:17 48
upstream1000.fa.gz 2019-10-17 18:18 18M
upstream1000.fa.gz.md5 2019-10-17 18:18 53
upstream2000.fa.gz 2019-10-17 18:18 35M
upstream2000.fa.gz.md5 2019-10-17 18:18 53
upstream5000.fa.gz 2019-10-17 18:20 97M
upstream5000.fa.gz.md5 2019-10-17 18:20 53
ponAbe2.fa.gz 2020-01-23 02:25 960M
genes/ 2020-10-02 13:38 -
ponAbe2.chromAlias.txt 2022-09-08 14:15 915
ponAbe2.chromAlias.bb 2022-09-08 14:15 41K