This directory contains the Build 2 Version 1 (UCSC version
panTro2) chimpanzee 6X draft assembly produced by the Chimp
Genome Sequencing Consortium.
Files included in this directory:
chromAgp.tar.gz - Description of how the chromosome-based assembly
was generated, unpacking to one file per chromosome.
chromFa.tar.gz - The working draft sequence in one file per chromosome.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are in lower case while non-repeating sequence is
in upper case. The main assembly is in the chrN.fa files where N
is the name of the chromosome. The chrN_random.fa files contain
clones which are either not yet finished, or which cannot be
placed with certainty at a specific place on the chromosome.
chromFaMasked.tar.gz - The working draft sequence in one file per
chromosome. Repeats are masked by capital N's and
non-repeating sequence is shown in upper case.
chromOut.tar.gz - RepeatMasker .out file for chromosomes, created
with RepeatMasker at the -s sensitive setting.
chromQuals.tar.gz - Quality scores for all bases in the assembly,
in one file per chromosome.
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep
repeats with period of less than or equal to 12, and translated
into one .bed file per chromosome.
est.fa.gz - Chimp and human ESTs in GenBank. This sequence data is
updated once a week via automatic GenBank updates.
panTro2.2bit - contains the complete chimp/panTro2 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
panTro2.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksum file
mrna.fa.gz - Chimp and human 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 RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could 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.
panTro2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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If you plan to download a large file or multiple files from this
directory, we recommend 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/bigZips. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
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 -
chromAgp.tar.gz 2006-04-03 17:24 6.3M
chromFa.tar.gz 2006-04-03 17:37 907M
chromFaMasked.tar.gz 2006-04-03 17:44 494M
chromOut.tar.gz 2006-04-03 17:45 156M
chromQuals.tar.gz 2006-07-17 15:33 416M
chromTrf.tar.gz 2006-04-03 17:45 6.6M
est.fa.gz 2019-10-17 17:01 2.7M
est.fa.gz.md5 2019-10-17 17:01 44
md5sum.txt 2009-06-10 10:24 566
mrna.fa.gz 2019-10-17 16:47 1.9M
mrna.fa.gz.md5 2019-10-17 16:47 45
panTro2.2bit 2006-03-24 14:05 832M
panTro2.chrom.sizes 2006-03-06 10:31 921
panTro2.fa.gz 2020-01-23 02:25 907M
panTro2.quals.fa.gz 2009-06-08 11:42 72M
refMrna.fa.gz 2019-10-17 17:01 1.5M
refMrna.fa.gz.md5 2019-10-17 17:01 48
upstream1000.fa.gz 2019-10-17 17:01 485K
upstream1000.fa.gz.md5 2019-10-17 17:01 53
upstream2000.fa.gz 2019-10-17 17:01 921K
upstream2000.fa.gz.md5 2019-10-17 17:01 53
upstream5000.fa.gz 2019-10-17 17:02 2.2M
upstream5000.fa.gz.md5 2019-10-17 17:02 53
xenoMrna.fa.gz 2019-10-17 16:56 6.8G
xenoMrna.fa.gz.md5 2019-10-17 16:57 49
xenoRefMrna.fa.gz 2019-10-17 17:01 329M
xenoRefMrna.fa.gz.md5 2019-10-17 17:01 52