This directory contains the Jan. 2018 (Susie_PABv2/ponAbe3) assembly of the
orangutan genome (ponAbe3, University of Washington),
as well as repeat annotations and GenBank sequences.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/325
https://www.ncbi.nlm.nih.gov/genome/assembly/1529631
https://www.ncbi.nlm.nih.gov/bioproject/369439
https://www.ncbi.nlm.nih.gov/bioproject/SAMN06275555
Files included in this directory:
ponAbe3.2bit - contains the complete orangutan/ponAbe3 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.soe.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
ponAbe3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
ponAbe3.agp.gz - Description of how the assembly was generated from
fragments.
ponAbe3.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.
ponAbe3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
ponAbe3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
February 01 2017 (open-4-0-7) 1.331 version of RepeatMasker
RepBase library: Dfam_Consensus RELEASE 20170127
CC RepBase RELEASE 20170127; *
ponAbe3.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.
est.fa.gz - Orangutan ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Orangutan mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might 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.
ponAbe3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
ponAbe3.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
ponAbe3.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
ponAbe3.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
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.soe.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/ponAbe3/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.soe.ucsc.edu/goldenPath/ponAbe3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/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
-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
ponAbe3.gc5Base.wigVarStep.gz 2018-03-25 22:59 1.5G
ponAbe3.fa.gz 2018-04-09 11:07 928M
ponAbe3.2bit 2018-03-26 10:37 762M
ponAbe3.gc5Base.wib 2019-01-17 14:53 580M
ponAbe3.fa.masked.gz 2018-04-09 11:16 465M
xenoRefMrna.fa.gz 2019-10-16 14:41 327M
ponAbe3.fa.out.gz 2018-04-09 10:52 168M
ponAbe3.gc5Base.wig.gz 2019-01-17 14:53 11M
est.fa.gz 2019-10-16 14:40 8.9M
ponAbe3.trf.bed.gz 2018-04-09 10:52 8.0M
upstream5000.fa.gz 2018-04-09 11:17 4.9M
mrna.fa.gz 2019-10-16 14:36 4.6M
refMrna.fa.gz 2019-10-16 14:41 3.4M
upstream2000.fa.gz 2018-04-09 11:16 2.0M
ponAbe3.chromAlias.bb 2022-09-08 14:15 1.5M
upstream1000.fa.gz 2018-04-09 11:16 1.1M
ponAbe3.chromAlias.txt 2022-09-08 14:15 262K
ponAbe3.chrom.sizes 2018-03-25 22:48 138K
ponAbe3.agp.gz 2018-04-09 10:51 79K
md5sum.txt 2019-01-17 15:58 692
xenoRefMrna.fa.gz.md5 2019-10-16 14:41 52
refMrna.fa.gz.md5 2019-10-16 14:41 48
mrna.fa.gz.md5 2019-10-16 14:36 45
est.fa.gz.md5 2019-10-16 14:40 44
genes/ 2020-04-27 14:08 -