This directory contains the Mar. 2006 chromosome-based chimpanzee
assembly produced by Washington University, St. Louis. It is
based on the Oct. 2005 6X draft assembly (Build 2 Version 1),
produced by the Chimpanzee Genome Sequencing Consortium.
The whole genome shotgun sequence data were assembled using PCAP
by the Washington University Genome Sequencing
Center. The underlying whole genome shotgun data were generated at the
Washington University School of Medicine and the Broad Institute.
A 5-megabase region of chromosome 7 was finished at the Washington
University Genome Sequencing Center (chr7:84674857-89461887). The
chromosome Y sequence was finished at the Washington University Genome
Sequencing Center with detailed mapping and extensive collaboration
with the Broad Institute.
This assembly also contains finished chromosome 21 sequence from the Riken
Genome Sciences Center.
Files included in this directory:
- chr*.fa.zip: compressed FASTA sequence of each chromosome.
Each chromosome is in a separate file in a zipped Fasta format.
Repeats -- which are shown in lower case -- are annotated by
RepeatMasker run at the sensitive setting. The RepeatMasker
version used was:
1.11 2006/01/20 (open 3-1-3)
The RepeatMasker pan_troglodytes library was used, with the
addition of 2 subtelomeric satellite repeats provided by
the Evan Eichler lab. The library version used was:
20060119
Tandem repeats of period 12 or less are also masked out
using Tandem Repeats Finder.
The main assembly is contained in the chrN.fa files, where N is the
name of the chromosome. The chrN_random.fa files contain sequence that
cannot be placed with certainty at a specific place on the chromosome.
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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/panTro2/chromosomes. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The chimp 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 -
chr1.fa.gz 2006-04-03 17:01 68M
chr1_random.fa.gz 2006-04-03 17:01 2.6M
chr2a.fa.gz 2006-04-03 17:13 33M
chr2a_random.fa.gz 2006-04-03 17:13 887K
chr2b.fa.gz 2006-04-03 17:13 40M
chr2b_random.fa.gz 2006-04-03 17:13 632K
chr3.fa.gz 2006-04-03 17:02 61M
chr3_random.fa.gz 2006-04-03 17:02 1.0M
chr4.fa.gz 2006-04-03 17:03 59M
chr4_random.fa.gz 2006-04-03 17:03 1.8M
chr5.fa.gz 2006-04-03 17:04 55M
chr5_random.fa.gz 2006-04-03 17:04 925K
chr6.fa.gz 2006-04-03 17:05 52M
chr6_hla_hap1.fa.gz 2006-04-03 17:13 2.7K
chr6_random.fa.gz 2006-04-03 17:05 2.7M
chr7.fa.gz 2006-04-03 17:05 47M
chr7_random.fa.gz 2006-04-03 17:05 2.0M
chr8.fa.gz 2006-04-03 17:06 43M
chr8_random.fa.gz 2006-04-03 17:06 2.2M
chr9.fa.gz 2006-04-03 17:07 34M
chr9_random.fa.gz 2006-04-03 17:07 2.1M
chr10.fa.gz 2006-04-03 17:08 39M
chr10_random.fa.gz 2006-04-03 17:08 2.2M
chr11.fa.gz 2006-04-03 17:08 39M
chr11_random.fa.gz 2006-04-03 17:09 2.4M
chr12.fa.gz 2006-04-03 17:09 40M
chr12_random.fa.gz 2006-04-03 17:09 661K
chr13.fa.gz 2006-04-03 17:10 28M
chr13_random.fa.gz 2006-04-03 17:10 2.8M
chr14.fa.gz 2006-04-03 17:10 27M
chr14_random.fa.gz 2006-04-03 17:10 611K
chr15.fa.gz 2006-04-03 17:10 24M
chr15_random.fa.gz 2006-04-03 17:10 914K
chr16.fa.gz 2006-04-03 17:11 23M
chr16_random.fa.gz 2006-04-03 17:11 1.7M
chr17.fa.gz 2006-04-03 17:11 23M
chr17_random.fa.gz 2006-04-03 17:11 1.4M
chr18.fa.gz 2006-04-03 17:11 23M
chr18_random.fa.gz 2006-04-03 17:11 520K
chr19.fa.gz 2006-04-03 17:12 16M
chr19_random.fa.gz 2006-04-03 17:12 591K
chr20.fa.gz 2006-04-03 17:12 18M
chr20_random.fa.gz 2006-04-03 17:12 500K
chr21.fa.gz 2006-04-03 17:12 10M
chr22.fa.gz 2006-04-03 17:12 10M
chr22_random.fa.gz 2006-04-03 17:12 342K
chrM.fa.gz 2006-04-03 17:07 5.4K
chrUn.fa.gz 2006-04-03 17:13 13M
chrX.fa.gz 2006-04-03 17:07 42M
chrX_random.fa.gz 2006-04-03 17:07 899K
chrY.fa.gz 2006-04-03 17:07 7.0M
chrY_random.fa.gz 2006-04-03 17:07 248K
md5sum.txt 2006-04-03 17:14 2.5K