This directory contains alignments of the following assemblies:
- target/reference: Mouse (mm9, Jul. 2007, NCBI Build 37)
- query: Rat (rn4, Nov. 2004, Baylor HGSC v. 3.4)
Files included in this directory:
- md5sum.txt: md5sum checksums for the files in this directory
- mm9.rn4.all.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html .
- mm9.rn4.net.gz: "net" file that describes rearrangements between
the species and the best Rat match to any part of the
Mouse genome. The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html .
- mm9.rn4.syn.net.gz: "syntenic net" file. This is the net
filtered to remove non-syntenic alignments
- axtNet/*.mm9.rn4.net.axt.gz: chained and netted alignments,
i.e. the best chains in the Mouse genome, with gaps in the best
chains filled in by next-best chains where possible. The axt format is
described in http://genome.ucsc.edu/goldenPath/help/axt.html .
The mm9 and rn4 assemblies were aligned by the blastz alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/). Any mm9 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 rn4,
with chunks of 10,000,000 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.
The blastz scoring matrix (Q parameter) used was:
A C G T
A 56 -109 -45 -137
C -109 100 -103 -45
G -45 -103 100 -109
T -137 -45 -109 56
with a gap open penalty of O=600 and a gap extension penalty of E=55.
The minimum score for an alignment to be kept was K=4500 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. Other blastz
parameters specifically set for this species pair:
E=55
O=600
T=2
Y=15000
The .lav format blastz output was translated to the .psl format with
lavToPsl, then chained by the axtChain program.
Chain minimum score: 5000, and linearGap matrix of (medium):
tableSize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300
Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz were 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/mm9/vsRn4/. To download multiple files, use the "mget"
command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all files in the current directory)
All files in this directory are freely available for public use.
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References
Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic
sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).
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
(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/ 2007-09-11 14:42 -
md5sum.txt 2007-11-07 13:58 2.4K
mm9.rn4.all.chain.gz 2007-08-31 16:17 189M
mm9.rn4.net.gz 2007-09-04 12:49 130M
mm9.rn4.syn.net.gz 2007-11-07 12:04 123M