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:

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:
    See also:

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

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

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

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:
         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
[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:// .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file:
    wget --timestamping 
        -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 - genes/ 2020-04-27 14:08 - est.fa.gz.md5 2019-10-16 14:40 44 mrna.fa.gz.md5 2019-10-16 14:36 45 refMrna.fa.gz.md5 2019-10-16 14:41 48 xenoRefMrna.fa.gz.md5 2019-10-16 14:41 52 md5sum.txt 2019-01-17 15:58 692 ponAbe3.agp.gz 2018-04-09 10:51 79K ponAbe3.chrom.sizes 2018-03-25 22:48 138K ponAbe3.chromAlias.txt 2022-09-08 14:15 262K upstream1000.fa.gz 2018-04-09 11:16 1.1M 2022-09-08 14:15 1.5M upstream2000.fa.gz 2018-04-09 11:16 2.0M refMrna.fa.gz 2019-10-16 14:41 3.4M mrna.fa.gz 2019-10-16 14:36 4.6M upstream5000.fa.gz 2018-04-09 11:17 4.9M ponAbe3.trf.bed.gz 2018-04-09 10:52 8.0M est.fa.gz 2019-10-16 14:40 8.9M ponAbe3.gc5Base.wig.gz 2019-01-17 14:53 11M ponAbe3.fa.out.gz 2018-04-09 10:52 168M xenoRefMrna.fa.gz 2019-10-16 14:41 327M ponAbe3.fa.masked.gz 2018-04-09 11:16 465M ponAbe3.gc5Base.wib 2019-01-17 14:53 580M ponAbe3.2bit 2018-03-26 10:37 762M ponAbe3.fa.gz 2018-04-09 11:07 928M ponAbe3.gc5Base.wigVarStep.gz 2018-03-25 22:59 1.5G