This directory contains alignments of the following assemblies:

  - target/reference: Bushbaby
    (otoGar3, Mar. 2011 (Broad/otoGar3),
    Broad Institute (GCA_000181295.3))

  - query: Mouse
    (mm39, Jun. 2020 (GRCm39/mm39),
    Genome Reference Consortium Mouse Build 39 (GCA_000001635.9))

Files included in this directory:

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

  - otoGar3.mm39.all.chain.gz: chained lastz alignments. The chain format is
    described in .

  - "net" file that describes rearrangements between
    the species and the best Mouse match to any part of the
    Bushbaby genome.  The net format is described in .

  - chained and netted alignments,
    i.e. the best chains in the Bushbaby genome, with gaps in the best
    chains filled in by next-best chains where possible.  The axt format is
    described in .

  - otoGar3.mm39.synNet.maf.gz - filtered net file for syntenic alignments
               only, in MAF format, see also, description of MAF format:

  - - filtered net file for syntenic alignments only

  - reciprocalBest/ directory, contains reciprocal-best netted chains
    for otoGar3-mm39

The chainSwap program was used to translate mm39-referenced chained lastz
alignments to otoGar3 into otoGar3-referenced chains aligned to mm39.  See
the download directory goldenPath/mm39/vsOtoGar3/README.txt for more
information about the mm39-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.

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, then go to the directory
goldenPath/otoGar3/vsMm39/. To download multiple files, use the "mget"

    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.


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

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 - md5sum.txt 2020-11-24 18:08 291 otoGar3.mm39.all.chain.gz 2020-11-24 17:27 164M 2020-11-24 17:37 576M 2020-11-24 17:50 146M 2020-11-24 17:57 137M otoGar3.mm39.synNet.maf.gz 2020-11-24 18:08 546M reciprocalBest/ 2021-03-15 16:06 -