This directory contains alignments of the chicken assembly
(galGal2, Feb. 2004) to the opossum assembly (monDom1, Oct. 2004).
Files included in this directory:
- chicken.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- chicken.net.gz: "net" file that describes rearrangements between
the species and the best chicken match to any part of the opossum
genome. The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.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 -90 -25 -100
C -90 100 -100 -25
G -25 -100 100 -90
T -100 -25 -90 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 5,000 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. Extra blastz
parameters:
H=2000 interpolate between alignments at threshold K = 2000.
K=2200 threshold for MSPs.
L=10000 threshold for gapped alignments.
Y=3400 X-drop parameter for gapped extension.
Each chromosome or scaffold was divided into 10,000,000 base chunks for the
blastz alignments. No lineage specific repeats were used in these alignments.
The .lav format blastz output, which does not include the sequence, was
converted to .axt with lavToAxt. Low scores can occur using the scoring
matrix above and with repeats abridged; therefore, alignments were rescored
using PSU's restore_rpts program and the default scoring 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
For chaining, the axtChain linearGap option was used to specify gap
penalties:
tablesize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
Chains produced by axtChain were also filtered with a minimum score of 5000
and then chainAntiRepeat was applied to remove chains that are primarily the
result of repeats and degenerate DNA.
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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/monDom1/vsGalGal2/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Preliminary drafts of the opossum sequence are made freely available
before scientific publication by the Broad Institute, 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 provider of this data
(The Broad Institute) is properly acknowledged.
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.
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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 -
chicken.net.gz 2005-01-13 17:07 18M
chicken.chain.gz 2005-01-13 16:55 29M