This directory contains alignments of the following assemblies:
- target/reference: Rat (rn4, Nov. 2004, Baylor HGSC v. 3.4)
- query: Rhesus (rheMac2, Jan. 2006, Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4)
Files included in this directory:
- md5sum.txt: md5sum checksums for the files in this directory
- rn4.rheMac2.all.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html .
- rn4.rheMac2.net.gz: "net" file that describes rearrangements between
the species and the best Rhesus match to any part of the
Rat genome. The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html .
- axtNet/*.rn4.rheMac2.net.axt.gz: chained and netted alignments,
i.e. the best chains in the Rat 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 rn4 and rheMac2 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 rn4 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 rheMac2,
with chunks of 50,000,000 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.
Transposons that have been inserted since the Rhesus/Rat split were
removed from the assemblies before alignment using the fasta-subseq and
strip_rpts programs from Penn State. The abbreviated genomes were aligned
with blastz, and the transposons were then added back in (i.e. the
alignment coordinates were adjusted) using the restore_rpts program from
Penn State.
The blastz scoring matrix (Q parameter) used was the default matrix:
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 O=400 and a gap extension penalty of E=30.
The minimum score for an alignment to be kept was K=3000 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.
The .lav format blastz output was translated to the .psl format with
lavToPsl, then chained by the axtChain program.
Chain minimum score: 3000, 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/rn4/vsRheMac2/. 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 -
rn4.rheMac2.all.chain.gz 2006-03-23 02:38 233M
rn4.rheMac2.net.gz 2006-03-23 04:39 122M
md5sum.txt 2006-03-23 04:50 3.3K
axtNet/ 2006-03-23 04:50 -