This directory contains alignments of the human assembly
(hg15, Apr. 2003) to the mouse assembly (mm3, Feb. 2003).
Files included in this directory:
- axtAll directory: all alignments
- axtBest directory: filtered set of only the best alignments for
a particular region in the mouse genome
- axtNet directory: 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: a highly conserved subset of the best
alignments for any part of the mouse genome
These alignments are in "axt" format. For a description, see
The alignments were produced by the blastz alignment program, which
is available from Webb Miller's lab at Penn State University
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was:
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 400 and a gap extension penalty of 30. The
minimum score for an alignment to be kept was 3000 for the first pass
and 2200 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.
Each chromosome was divided into 10,010,000 base chunks with 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt.
The axtNet alignments were processed with chainNet, netSyntenic,
and netClass written by Jim Kent at UCSC. The axtTight alignments were
processed with subsetAxt from Jim Kent 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. The axtTight subset covers 6% of the mouse
genome while axtBest covers 40%.
If you plan to download a large file or multiple files from this
directory, we recommend that 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/mm3/alignments/vsHg15. To download
multiple files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the files in this directory are freely usable for any purpose.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80