This directory contains alignments of the following assemblies:

  - target/reference: Mouse (mm6, March 2005, NCBI Build 34)

  - query: Dog (canFam1, Jul. 2004, Broad Institute v. 1.0)

Files included in this directory:

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

  - mm6.canFam1.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - mm6.canFam1.net.gz: "net" file that describes rearrangements between 
    the species and the best Dog match to any part of the
    Mouse genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.mm6.canFam1.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Mouse 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 .

  - mm6.canFam1.over.chain.gz: chained and netted alignments in chain format.

The mm6 and canFam1 assemblies were aligned by the blastz alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/).  Any mm6 sequences larger
than 10,010,000 bases were split into chunks of 10,010,000 bases overlapping
by 10,000 bases for alignment.  A similar process was followed for canFam1,
with chunks of 10,000,000 overlapping by 0.)  Following alignment, the
coordinates of the chunk alignments were corrected by the
blastz-normalizeLav script written by Scott Schwartz of Penn State. 
Transposons that have been inserted since the Dog/Mouse split were
removed from the assemblies before alignment using the fasta-subseq and
strip_rpts programs from Penn State.  The abbreviated genomes were aligned
with blastz, and the transposons were then added back in (i.e. the
alignment coordinates were adjusted) using the restore_rpts program from
Penn State.

The blastz scoring matrix (Q parameter) used was the default matrix:

           A    C    G    T
      A   91 -114  -31 -123
      C -114  100 -125  -31
      G  -31 -125  100 -114
      T -123  -31 -114   91

with a gap open penalty of O=400 and a gap extension penalty of E=30.
The minimum score for an alignment to be kept was K=3000 for the first pass
and L=2200 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.  The minimum
score for alignments to be interpolated between was H=2000.  

The .lav format blastz output was translated to the .psl format with
lavToPsl, then chained by the axtChain program.

Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs. Best chains (.over.chain) were extracted from the
nets and the set of all chained alignments by the netChainSubset program.
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 hgdownload.cse.ucsc.edu, then go to the directory
goldenPath/mm6/vsCanFam1/. 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

Chiaromonte, F., Yap, V.B., and Miller, W.  Scoring pairwise genomic
sequence alignments.  Pac Symp Biocomput 2002, 115-26 (2002).

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489
(2003).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W.  Human-mouse alignments with BLASTZ</A>.
Genome Res. 13(1), 103-7 (2003).

      Name                     Last modified      Size  Description
      Parent Directory                              -   
      mm6.canFam1.net.gz       2005-04-03 15:00  115M  
      mm6.canFam1.all.chain.gz 2005-04-03 13:43  195M  
      md5sum.txt               2005-04-03 15:09  3.0K  
      axtNet/                  2005-04-03 15:08    -