This directory contains alignments of the following assemblies:

  - target/reference: Whipworm
    (triSui1, Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1),
    University of Melboure T. suis (male) genome project)

  - query: Trichinella
    (triSpi1, Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1),
    WashU School of Medicine T. spiralis genome project)

Files included in this directory:

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

  - triSui1.triSpi1.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - triSui1.triSpi1.net.gz: "net" file that describes rearrangements between
    the species and the best Trichinella match to any part of the
    Whipworm genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - triSui1.triSpi1.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Whipworm 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 .

  - triSui1.triSpi1.synNet.maf.gz - filtered net file for syntenic alignments
               only, in MAF format, see also, description of MAF format:
               http://genome.ucsc.edu/FAQ/FAQformat.html#format5

  - triSui1.triSpi1.syn.net.gz - filtered net file for syntenic alignments only

  - reciprocalBest/ directory, contains reciprocal-best netted chains
    for triSui1-triSpi1

The chainSwap program was used to translate triSpi1-referenced chained blastz
alignments to triSui1 into triSui1-referenced chains aligned to triSpi1.  See
the download directory goldenPath/triSpi1/vsTriSui1/README.txt for more
information about the triSpi1-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/triSui1/vsTriSpi1/. 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.