This directory contains the Nov. 2008 (Baylor Pham_1.0/papHam1) assembly of the baboon genome
(papHam1, Baylor BCM HGSC Pham_1.0), as well as repeat annotations and GenBank sequences.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/778
http://www.ncbi.nlm.nih.gov/genome/assembly/N/A
http://www.ncbi.nlm.nih.gov/bioproject/20425
Files included in this directory:
papHam1.2bit - contains the complete baboon/papHam1 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
papHam1.agp.gz - Description of how the assembly was generated from
fragments.
papHam1.fa.gz - "Soft-masked" assembly sequence in one file.
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.
papHam1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
papHam1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
April 26 2011 (open-3-3-0) version of RepeatMasker
RepBase library: RELEASE 20110920
papHam1.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Baboon mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
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.
papHam1.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 that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/papHam1/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/papHam1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/papHam1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papHam1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papHam1/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
For conditions of use regarding the Baboon genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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Name Last modified Size Description
Parent Directory -
genes/ 2020-02-05 13:47 -
md5sum.txt 2012-07-13 14:09 304
mrna.fa.gz 2019-10-16 14:17 192K
mrna.fa.gz.md5 2019-10-16 14:17 45
papHam1.2bit 2009-05-20 13:40 732M
papHam1.agp.gz 2012-07-13 13:38 13M
papHam1.chrom.sizes 2009-05-11 09:46 6.4M
papHam1.fa.gz 2012-07-13 13:54 867M
papHam1.fa.masked.gz 2012-07-13 14:03 475M
papHam1.fa.out.gz 2012-07-13 13:40 167M
papHam1.trf.bed.gz 2012-07-13 13:40 8.3M
refMrna.fa.gz 2019-10-16 14:18 271K
refMrna.fa.gz.md5 2019-10-16 14:18 48
upstream1000.fa.gz 2019-10-16 14:20 12M
upstream1000.fa.gz.md5 2019-10-16 14:20 53
upstream2000.fa.gz 2019-10-16 14:23 22M
upstream2000.fa.gz.md5 2019-10-16 14:23 53
upstream5000.fa.gz 2019-10-16 14:25 56M
upstream5000.fa.gz.md5 2019-10-16 14:25 53
xenoMrna.fa.gz 2016-03-21 07:30 5.0G
xenoMrna.fa.gz.md5 2016-03-21 07:30 49
xenoRefMrna.fa.gz 2019-10-16 14:17 331M
xenoRefMrna.fa.gz.md5 2019-10-16 14:17 52