This directory contains alignments of the following assemblies:

  - target/reference: Gibbon (nomLeu1, Jan. 2010 (GGSC Nleu1.0/nomLeu1), GGSC (NCBI project 13974, accession GCA_000146795.1))

  - query: Gorilla (gorGor3, May 2011 (gorGor3.1/gorGor3), Wellcome Trust Sanger Institute May 2011 (NCBI project 31265, GCA_000151905.1))

Files included in this directory:

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

  - nomLeu1.gorGor3.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - nomLeu1.gorGor3.net.gz: "net" file that describes rearrangements between 
    the species and the best Gorilla match to any part of the
    Gibbon genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - nomLeu1.gorGor3.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Gibbon 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 gorGor3-referenced chained blastz
alignments to nomLeu1 into nomLeu1-referenced chains aligned to gorGor3.  See
the download directory goldenPath/gorGor3/vsNomLeu1/README.txt for more
information about the gorGor3-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/nomLeu1/vsGorGor3/. 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

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
Ph.D. Thesis, The Pennsylvania State University

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.