This directory contains alignments of the following assemblies:

  - target/reference: Human (hg18, Mar. 2006, NCBI Build 36.1)

  - query: Chimp (panTro2, Jan. 2006, Washington University Build 2 Version 1)

Files included in this directory:

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

  - hg18.panTro2.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - hg18.panTro2.net.gz: "net" file that describes rearrangements between 
    the species and the best Chimp match to any part of the
    Human genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - hg18.panTro2.rbest.net.gz: "net" file containing only reciprocal
    best alignment chains.   This is produced by extracting the chains
    from the panTro2.hg18 alignment net and then netting these
    with hg18 as the target, so that only the best human alignments
    to chimp that are also the best in human are retained.
    
  - hg18.panTro2.rbest.chain.gz: reciprocal best chained blastz alignments. 
    These chains are extracted from the reciprocal best net file.

  - axtNet/*.hg18.panTro2.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Human 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 .

  - axtRBestNet/*.hg18.panTro2.net.axt.gz: reciprocal best chained and netted alignments,
    i.e. the best chains in the Human genome that are also the best matches
    in the Chimp genome.  These are obtained from the reciprocal best chains.

The chainSwap program was used to translate panTro2-referenced chained blastz
alignments to hg18 into hg18-referenced chains aligned to panTro2.  See
the download directory goldenPath/panTro2/vsHg18/README.txt for more
information about the panTro2-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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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 hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/vsPanTro2

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

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

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References

Chiaromonte, F., Yap, V.B., and Miller, W.  Scoring pairwise genomic
sequence alignments.  Pac Symp Biocomput 2002, 115-26 (2002).

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489
(2003).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W.  Human-mouse alignments with BLASTZ</A>.
Genome Res. 13(1), 103-7 (2003).