This directory contains alignments of the human assembly (hg17,
May 2004) to the mouse assembly (mm5, May 2004).
Files included in this directory:
- 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 mouse genome.
- human.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- human.net.gz: "net" file that describes rearrangements between the
species and the best human match to any part of the mouse genome.
The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html.
- md5sum.txt: checksums of the files in this directory
The alignments in the axtNet and axtTight directories are in "axt"
format. For a description, see
http://genome.ucsc.edu/goldenPath/help/axt.html.
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.
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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/mm5/vsHg17. 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.
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References
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/ 2004-07-13 14:54 -
axtTight/ 2004-07-13 10:07 -
md5sum.txt 2004-09-08 12:35 5.0K
human.net.gz 2004-07-08 22:40 142M
human.chain.gz 2004-07-08 13:32 295M