This directory contains alignments of the following assemblies:

  - target/reference: Orangutan
    (ponAbe3, Jan. 2018 (Susie_PABv2/ponAbe3),
    University of Washington)

  - query: Human
    (hg19, Feb. 2009 (GRCh37/hg19),
    GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1))

Files included in this directory:

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

  - ponAbe3.hg19.all.chain.gz: chained lastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - ponAbe3.hg19.net.gz: "net" file that describes rearrangements between
    the species and the best Human match to any part of the
    Orangutan genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - ponAbe3.hg19.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Orangutan 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 .

  - ponAbe3.hg19.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

  - ponAbe3.hg19.syn.net.gz - filtered net file for syntenic alignments only

  - reciprocalBest/ directory, contains reciprocal-best netted chains
    for ponAbe3-hg19

The chainSwap program was used to translate hg19-referenced chained lastz
alignments to ponAbe3 into ponAbe3-referenced chains aligned to hg19.  See
the download directory goldenPath/hg19/vsPonAbe3/README.txt for more
information about the hg19-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/ponAbe3/vsHg19/. 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                                -   
      ponAbe3.hg19.all.chain.gz  2018-12-14 14:45   64M  
      ponAbe3.hg19.net.axt.gz    2018-12-14 15:05  1.4G  
      ponAbe3.hg19.net.gz        2018-12-14 15:25   44M  
      ponAbe3.hg19.syn.net.gz    2018-12-14 15:27   43M  
      ponAbe3.hg19.synNet.maf.gz 2018-12-14 15:47  1.4G  
      md5sum.txt                 2018-12-14 15:47  291   
      reciprocalBest/            2021-06-30 14:28    -