This directory contains alignments of the following assemblies:

  - target/reference: Rhesus (rheMac3, Oct. 2010 (BGI CR_1.0/rheMac3),
    Beijing Genomics Institute, Shenzhen (GCA_000230795.1))

  - query: Rat (rn5, Mar. 2012 (RGSC 5.0/rn5), RGSC Rnor_5.0 (GCA_000001895.3))

Files included in this directory:

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

  - rheMac3.rn5.all.chain.gz: chained blastz alignments. The chain format is
    described in .

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

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

The chainSwap program was used to translate rn5-referenced chained blastz
alignments to rheMac3 into rheMac3-referenced chains aligned to rn5.  See
the download directory goldenPath/rn5/vsRheMac3/README.txt for more
information about the rn5-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.

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/rheMac3/vsRn5/. 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.


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 2012-12-03 18:17 169 rheMac3.rn5.all.chain.gz 2012-07-19 08:47 162M 2012-07-19 09:12 636M 2012-07-19 09:30 171M