This directory contains alignments of the dog assembly
(canFam, Jul. 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.
- dog.chain.zip: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- dog.net.zip: "net" file that describes rearrangements between the
species and the best mouse match to any part of the dog genome.
The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html.
- dogSyn.net.zip:
The alignments in the axtNet directory 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.
----------------------------------------------------------------
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/vsCanFam1. 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. The dog sequence is made freely available before scientific
publication with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged
in databases.
2. Users are free to use the data in scientific papers analyzing
particular genes and regions if the providers of these data are
properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html
for credit information.
3. The centers producing the data reserve the right to publish the
initial large-scale analyses of the data set, including large-scale
identification of regions of evolutionary conservation and large-scale
genomic assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
--------------------------------------------------------------------
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/ 2004-07-19 11:27 -
md5sum.txt 2004-07-19 11:47 2.5K
dog.net.zip 2004-07-19 11:41 122M
dog.chain.zip 2004-07-19 11:39 202M