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: Rat
    (rn5, Mar. 2012 (RGSC 5.0/rn5),
    RGSC Rnor_5.0 (GCA_000001895.3))

Files included in this directory:

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

  - panTro4.rn5.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - panTro4.rn5.net.gz: "net" file that describes rearrangements between 
    the species and the best Rat match to any part of the
    Chimp genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - panTro4.rn5.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 .

The chainSwap program was used to translate rn5-referenced chained blastz
alignments to panTro4 into panTro4-referenced chains aligned to rn5.  See
the download directory goldenPath/rn5/vsPanTro4/README.txt for more
information about the rn5-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.

----------------------------------------------------------------
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/vsRn5/. 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.

--------------------------------------------------------------------
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               2012-12-04 10:32  169   
      panTro4.rn5.net.gz       2012-12-04 10:20  179M  
      panTro4.rn5.net.axt.gz   2012-12-04 09:58  666M  
      panTro4.rn5.all.chain.gz 2012-12-04 09:26  178M