This directory contains alignments of the following assemblies:

  - target/reference: Elephant
    (loxAfr3, Jul. 2009 (Broad/loxAfr3),
    Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000))

  - query: Hawaiian monk seal
    (neoSch1, Jun. 2017 (ASM220157v1/neoSch1),
    Johns Hopkins University)

Files included in this directory:

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

  - loxAfr3.neoSch1.all.chain.gz: chained lastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - loxAfr3.neoSch1.net.gz: "net" file that describes rearrangements between
    the species and the best Hawaiian monk seal match to any part of the
    Elephant genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - loxAfr3.neoSch1.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Elephant 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 .

  - loxAfr3.neoSch1.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

  - loxAfr3.neoSch1.syn.net.gz - filtered net file for syntenic alignments only

  - reciprocalBest/ directory, contains reciprocal-best netted chains
    for loxAfr3-neoSch1

The chainSwap program was used to translate neoSch1-referenced chained lastz
alignments to loxAfr3 into loxAfr3-referenced chains aligned to neoSch1.  See
the download directory goldenPath/neoSch1/vsLoxAfr3/README.txt for more
information about the neoSch1-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/loxAfr3/vsNeoSch1/. 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

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.

      Name                          Last modified      Size  Description
      Parent Directory                                   -   
      loxAfr3.neoSch1.all.chain.gz  2020-07-15 21:04  459M  
      loxAfr3.neoSch1.net.axt.gz    2020-07-15 21:21  934M  
      loxAfr3.neoSch1.net.gz        2020-07-15 21:42  183M  
      loxAfr3.neoSch1.syn.net.gz    2020-07-15 21:53  172M  
      loxAfr3.neoSch1.synNet.maf.gz 2020-07-15 22:12  895M  
      md5sum.txt                    2020-07-15 22:12  306