This directory contains the May. 2012 (Max-Planck/panPan1) assembly of the
    bonobo genome (panPan1, Max-Planck Institute panpan1 (GCA_000258665.1)),
    as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:

Files included in this directory:

panPan1.2bit - contains the complete bonobo/panPan1 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:

panPan1.agp.gz - Description of how the assembly was generated from

panPan1.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.

panPan1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

panPan1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    January 31 2015 (open-4-0-5) version of RepeatMasker
    RepBase library: RELEASE 20140131

panPan1.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

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Bonobo 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.

panPan1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

panPan1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
panPan1.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
panPan1.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

panPan1.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/panPan1/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 - panPan1.chrom.sizes 2013-02-28 15:55 188K panPan1.gc5Base.wigVarStep.gz 2013-02-28 16:10 1.3G panPan1.2bit 2013-03-07 11:36 804M panPan1.agp.gz 2015-01-06 09:35 2.9M panPan1.fa.out.gz 2015-01-06 09:36 152M panPan1.trf.bed.gz 2015-01-06 09:36 5.9M panPan1.fa.gz 2015-01-06 09:51 869M panPan1.fa.masked.gz 2015-01-06 10:02 602M panPan1.gc5Base.wib 2019-01-17 14:51 525M panPan1.gc5Base.wig.gz 2019-01-17 14:51 11M md5sum.txt 2019-01-17 15:57 479 mrna.fa.gz 2019-10-17 15:32 49K mrna.fa.gz.md5 2019-10-17 15:32 45 xenoRefMrna.fa.gz 2019-10-17 15:32 331M xenoRefMrna.fa.gz.md5 2019-10-17 15:32 52 refMrna.fa.gz 2019-10-17 15:32 42K refMrna.fa.gz.md5 2019-10-17 15:32 48 genes/ 2020-02-05 13:47 - panPan1.chromAlias.txt 2022-09-08 14:14 447K 2022-09-08 14:14 2.5M