This directory contains alignments of the mouse assembly (mm3, Feb. 2003)
to the human assembly (hg16, Jul. 2003).

  - target/reference: Human (hg16, Jul. 2003, NCBI Build 34)

  - query: Mouse (mm3, Feb. 2003, NCBI Build 30)

Files included in this directory:

  - md5sum.txt: md5sum checksums for the files in the axtNet, axtTight, chain 
    and net directories.

  - axtNet directory: contains chained and netted alignments, i.e. the
    best chains in the genome, with gaps in the best chains filled in
    by next-best chains where possible.

  - axtTight directory: contains a highly conserved subset of the best
    alignments for any part of the human genome.

  - chain directory: chained blastz alignments. The chain format is 
    described in

  - net directory: "net" files that describe rearrangements between the 
    species and the best chicken match to any part of the human genome.  
    The net format is described in

The hg16 and mm3 assemblies were aligned by the blastz alignment
program, which is available from Webb Miller's lab at Penn State
University (  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 rn3,
with chunks of 30,000,000 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 Human/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

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, which does not include the sequence, was 
converted to .axt with lavToAxt and then to .psl format using the axtToPsl
program. Blastz alignments were chained using the axtChain program. Chained 
alignments were processed into nets by the chainPreNet, chainNet, netSyntenic, 
and netClass programs. netToAxt was used to produce .axt files from the .net
and .chain files using the -maxGap=300 option. 
The axtTight alignments were processed with subsetAxt using the matrix:

         A    C    G    T
    A  100 -200 -100 -200
    C -200  100 -200 -100
    G -100 -200  100 -200
    T -200 -100 -200  100

with a gap open penalty of 2000 and a gap extension penalty of 50.
The minimum score was 3400.
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/hg16/vsMm3/. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

All the tables in this directory are freely available for public use.


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

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 
Sep 30 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 - axtNet/ 2006-03-16 13:51 - axtTight/ 2006-03-16 13:48 - chain/ 2006-03-14 09:20 - md5sum.txt 2006-03-16 14:05 9.2K net/ 2006-03-14 09:52 -