This directory contains the Build 1 Version 1 (UCSC version
panTro1) chimpanzee Arachne assembly produced by the Chimp
Genome Sequencing Consortium.
Files included in this directory:
panTro1.2bit - contains the complete chimp/panTro1 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.zip - Description of how the chromosome-based assembly
was generated, unpacking to one file per chromosome.
chromFa.zip - 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.zip - 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.zip - RepeatMasker .out file for chromosomes, created
with RepeatMasker at the -s sensitive setting.
chromQuals.zip - Quality scores for all bases in the assembly,
in one file per chromosome
est.fa.gz - Chimp ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksum file
mrna.fa.gz - Chimp mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
scaffolds.lft.zip - Offsets of scaffolds within chromosomes
and their orientation on + or - strand, generated from the
chromosome AGP files.
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.
panTro1.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/panTro1/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 -
panTro1.chrom.sizes 2004-01-26 11:35 952
chromOut.zip 2004-02-03 13:55 146M
chromAgp.zip 2004-02-12 15:30 941K
chromFa.zip 2004-02-12 15:57 875M
chromFaMasked.zip 2004-02-12 16:20 495M
scaffolds.lft.zip 2004-02-12 16:20 416K
chromQuals.zip 2004-07-06 20:44 466M
panTro1.2bit 2005-04-30 10:59 1.1G
md5sum.txt 2014-02-03 10:24 340
xenoMrna.fa.gz 2016-02-27 07:59 5.0G
xenoMrna.fa.gz.md5 2016-02-27 08:00 49
mrna.fa.gz 2019-10-17 17:04 1.9M
mrna.fa.gz.md5 2019-10-17 17:04 45
est.fa.gz 2019-10-17 17:09 2.7M
est.fa.gz.md5 2019-10-17 17:09 44
xenoRefMrna.fa.gz 2019-10-17 17:09 329M
xenoRefMrna.fa.gz.md5 2019-10-17 17:09 52
refMrna.fa.gz 2019-10-17 17:09 1.5M
refMrna.fa.gz.md5 2019-10-17 17:09 48
upstream1000.fa.gz 2019-10-17 17:10 3.2M
upstream1000.fa.gz.md5 2019-10-17 17:10 53
upstream2000.fa.gz 2019-10-17 17:10 6.0M
upstream2000.fa.gz.md5 2019-10-17 17:10 53
upstream5000.fa.gz 2019-10-17 17:11 14M
upstream5000.fa.gz.md5 2019-10-17 17:11 53
panTro1.fa.gz 2020-01-23 02:24 874M