This directory contains alignments of the following assemblies:

  - target/reference: Horse
    (equCab2, Sep. 2007 (Broad/equCab2),
    Broad Institute EquCab2)

  - query: Cow
    (bosTau8, Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8),
    University of Maryland Bos_taurus_UMD_3.1.1)

Files included in this directory:

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

  - equCab2.bosTau8.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - equCab2.bosTau8.net.gz: "net" file that describes rearrangements between
    the species and the best Cow match to any part of the
    Horse genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.equCab2.bosTau8.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Horse 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 bosTau8-referenced chained blastz
alignments to equCab2 into equCab2-referenced chains aligned to bosTau8.  See
the download directory goldenPath/bosTau8/vsEquCab2/README.txt for more
information about the bosTau8-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/equCab2/vsBosTau8/. 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                                  -   
      axtNet/                      2014-12-12 12:11    -   
      reciprocalBest/              2014-12-13 17:02    -   
      md5sum.txt                   2014-12-12 12:11  2.6K  
      equCab2.bosTau8.net.gz       2014-12-12 11:51  172M  
      equCab2.bosTau8.all.chain.gz 2014-12-12 10:18  575M