This directory contains alignments of the human assembly (hg17,
May 2004) to the rat assembly (rn3, Jun. 2003).
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
- 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
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 5000 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 rat
genome while axtBest covers 40%.
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/rnJun2003/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.
The rat data are made available before scientific publication with the
1. The data may be freely downloaded, used in analyses, and repackaged
2. Users are free to use the data in scientific papers analyzing
particular genes and regions if the providers of this data (the Rat
Genome Sequencing Consortium) are properly acknowledged.
3. The Centers producing the data reserve the right to publish the
initial large-scale analyses of the dataset, 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. This is in accordance with, and with the understandings in the Fort
Lauderdale meeting discussing Community Resource Projects (see
http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting
NHGRI policy statement
5. Any redistribution of the data should carry this notice.
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