This directory contains the Jul. 2007 assembly of the orangutan genome
(ponAbe2, WUSTL Pongo_albelii-2.0.2) in one gzip-compressed FASTA file
per chromosome.
This assembly was produced by the Genome Sequencing Center at the Washington
University School of Medicine in St. Louis.
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:
- chr*.fa.gz: compressed FASTA sequence of each 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.
RepeatMasker was run with the -s (sensitive) setting.
RepeatMasker version May 17 2007 (open-3-1-8)
library version RELEASE 20061006
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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/ponAbe2/chromosomes. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
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Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/ .
For a single file, e.g. chrM.fa.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/chrM.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/chrM.fa.gz'
-O chrM.fa.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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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 -
chr1.fa.gz 2007-10-01 17:26 67M
chr1_random.fa.gz 2007-10-01 17:32 10M
chr2a.fa.gz 2007-10-01 17:30 33M
chr2a_random.fa.gz 2007-10-01 17:32 3.9M
chr2b.fa.gz 2007-10-01 17:29 39M
chr2b_random.fa.gz 2007-10-01 17:32 4.2M
chr3.fa.gz 2007-10-01 17:26 60M
chr3_random.fa.gz 2007-10-01 17:32 5.8M
chr4.fa.gz 2007-10-01 17:27 58M
chr4_random.fa.gz 2007-10-01 17:32 6.5M
chr5.fa.gz 2007-10-01 17:27 54M
chr5_h2_hap1.fa.gz 2007-10-01 17:33 16K
chr5_random.fa.gz 2007-10-01 17:32 5.0M
chr6.fa.gz 2007-10-01 17:28 51M
chr6_cox_hap1.fa.gz 2007-10-01 17:33 393K
chr6_cox_hap1_random.fa.gz 2007-10-01 17:33 74K
chr6_qbl_hap2.fa.gz 2007-10-01 17:33 189K
chr6_qbl_hap2_random.fa.gz 2007-10-01 17:33 36K
chr6_random.fa.gz 2007-10-01 17:32 3.8M
chr7.fa.gz 2007-10-01 17:28 45M
chr7_random.fa.gz 2007-10-01 17:32 5.4M
chr8.fa.gz 2007-10-01 17:28 44M
chr8_random.fa.gz 2007-10-01 17:32 4.3M
chr9.fa.gz 2007-10-01 17:29 34M
chr9_random.fa.gz 2007-10-01 17:32 3.8M
chr10.fa.gz 2007-10-01 17:29 39M
chr10_random.fa.gz 2007-10-01 17:32 8.8M
chr11.fa.gz 2007-10-01 17:30 39M
chr11_random.fa.gz 2007-10-01 17:33 1.8M
chr12.fa.gz 2007-10-01 17:29 40M
chr12_random.fa.gz 2007-10-01 17:32 3.3M
chr13.fa.gz 2007-10-01 17:30 30M
chr13_random.fa.gz 2007-10-01 17:32 2.9M
chr14.fa.gz 2007-10-01 17:30 27M
chr14_random.fa.gz 2007-10-01 17:32 2.1M
chr15.fa.gz 2007-10-01 17:31 24M
chr15_random.fa.gz 2007-10-01 17:32 3.1M
chr16.fa.gz 2007-10-01 17:31 22M
chr16_random.fa.gz 2007-10-01 17:32 3.5M
chr17.fa.gz 2007-10-01 17:31 21M
chr17_random.fa.gz 2007-10-01 17:32 5.1M
chr18.fa.gz 2007-10-01 17:31 23M
chr18_random.fa.gz 2007-10-01 17:32 1.9M
chr19.fa.gz 2007-10-01 17:31 16M
chr19_random.fa.gz 2007-10-01 17:32 2.2M
chr20.fa.gz 2007-10-01 17:31 18M
chr20_random.fa.gz 2007-10-01 17:33 1.5M
chr21.fa.gz 2007-10-01 17:32 10M
chr21_random.fa.gz 2007-10-01 17:33 1.2M
chr22.fa.gz 2007-10-01 17:32 9.4M
chr22_random.fa.gz 2007-10-01 17:33 1.0M
chrM.fa.gz 2007-10-01 17:33 5.4K
chrUn.fa.gz 2007-10-01 17:31 18M
chrX.fa.gz 2007-10-01 17:28 46M
chrX_random.fa.gz 2007-10-01 17:32 2.8M
md5sum.txt 2007-10-01 18:12 2.7K