This directory contains alignments of the following assemblies:

  - target/reference: Dog
    (canFam4, Mar. 2020 (UU_Cfam_GSD_1.0/canFam4),
    Uppsala University)

  - query: Dog
    (canFam3, Sep. 2011 (Broad CanFam3.1/canFam3),
    Broad CanFam3.1 (GCA_000002285.2))

Files included in this directory:

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

  - canFam4.canFam3.all.chain.gz: chained lastz alignments. The chain format is
    described in .

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

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

  - canFam4.canFam3.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 canFam4-canFam3

The chainSwap program was used to translate canFam3-referenced chained lastz
alignments to canFam4 into canFam4-referenced chains aligned to canFam3.  See
the download directory goldenPath/canFam3/vsCanFam4/README.txt for more
information about the canFam3-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/canFam4/vsCanFam3/. 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 - canFam4.canFam3.all.chain.gz 2020-05-13 08:52 2.5G 2020-05-13 09:19 1.3G 2020-05-13 11:07 16M 2020-05-13 12:04 14M canFam4.canFam3.synNet.maf.gz 2020-05-13 12:29 1.3G md5sum.txt 2020-06-26 15:24 306 reciprocalBest/ 2020-07-07 18:32 -