This directory contains alignments of the following assemblies:

  - target/reference: Opossum
    (monDom5, Oct. 2006 (Broad/monDom5),
    Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000))

  - query: Black flying-fox
    (pteAle1, Aug 2012 (ASM32557v1/pteAle1),
    BGI GCA_000325575.1)

Files included in this directory:

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

  - monDom5.pteAle1.all.chain.gz: chained lastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - monDom5.pteAle1.net.gz: "net" file that describes rearrangements between
    the species and the best Black flying-fox match to any part of the
    Opossum genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.monDom5.pteAle1.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Opossum 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 .

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

  - reciprocalBest/ directory, contains reciprocal-best netted chains
    for monDom5-pteAle1

The chainSwap program was used to translate pteAle1-referenced chained lastz
alignments to monDom5 into monDom5-referenced chains aligned to pteAle1.  See
the download directory goldenPath/pteAle1/vsMonDom5/README.txt for more
information about the pteAle1-referenced lastz 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 lastz 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.soe.ucsc.edu, then go to the directory
goldenPath/monDom5/vsPteAle1/. 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.