This directory contains alignments of the following assemblies:

  - target/reference: Chimp
    (panTro4, Feb. 2011 (CSAC 2.1.4/panTro4),
    CSAC Pan_troglodytes-2.1.4 (GCA_000001515.4))

  - query: Bonobo
    (panPan2, Aug. 2015 (MPI-EVA panpan1.1/panPan2),
    Max-Planck Institute for Evolutionary Anthropology)

Files included in this directory:

  - md5sum.txt: md5sum checksums for the files in this directory

  - panTro4.panPan2.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - panTro4.panPan2.net.gz: "net" file that describes rearrangements between
    the species and the best Bonobo match to any part of the
    Chimp genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - panTro4.panPan2.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Chimp genome, with gaps in the best
    chains filled in by next-best chains where possible.  The axt format is
    described in http://genome.ucsc.edu/goldenPath/help/axt.html .

  - panTro4.panPan2.synNet.maf.gz - filtered net file for syntenic alignments
               only, in MAF format, see also, description of MAF format:
               http://genome.ucsc.edu/FAQ/FAQformat.html#format5

  - panTro4.panPan2.syn.net.gz - filtered net file for syntenic alignments only

  - reciprocalBest/ directory, contains reciprocal-best netted chains
    for panTro4-panPan2

The chainSwap program was used to translate panPan2-referenced chained blastz
alignments to panTro4 into panTro4-referenced chains aligned to panPan2.  See
the download directory goldenPath/panPan2/vsPanTro4/README.txt for more
information about the panPan2-referenced blastz and chaining process.

Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz were written by Jim Kent at UCSC.

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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/panTro4/vsPanPan2/. To download multiple files, use the "mget"
command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all files in the current directory)

All files in this directory are freely available for public use.

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References

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence
alignments. Pac Symp Biocomput.  2002:115-26.

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep
30;100(20):11484-9.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome
Res. 2003 Jan;13(1):103-7.

      Name                          Last modified      Size  Description
Parent Directory - md5sum.txt 27-May-2016 12:15 306 panTro4.panPan2.all.chain.gz 27-May-2016 10:41 43M panTro4.panPan2.net.axt.gz 27-May-2016 11:16 1.3G panTro4.panPan2.net.gz 27-May-2016 11:44 28M panTro4.panPan2.syn.net.gz 27-May-2016 11:46 25M panTro4.panPan2.synNet.maf.gz 27-May-2016 12:15 1.2G reciprocalBest/ 27-May-2016 15:50 -