This directory contains chained and netted alignments of the human
assembly (hg17, May 2004) to the zebrafish assembly (danRer1, Nov. 2003).
These alignments show the best chains in the genome, with gaps in the
best chains filled in by next-best chains where possible.
The alignments are in "axt" format. For a description, see
http://genome.ucsc.edu/goldenPath/help/axt.html. The chain format is
described at http://genome.ucsc.edu/goldenPath/help/chain.html and
the net format is described at
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 6000 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 10,000,000 base chunks for the blastz
alignments and all repeats for each organism were used as lineage-specific
repeats. Repeats were detected with Arian Smit's RepeatMasker program using
a zebrafish repeats library. 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
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/hg17/vsDanRer1/. 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 available for public use.
--------------------------------------------------------------------
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 -
chr6_hla_hap1.axt.gz 2005-08-16 16:55 619
chr6_hla_hap2.axt.gz 2005-08-16 16:55 1.8K
chr18_random.axt.gz 2005-08-16 16:53 2.2K
md5sum.txt 2006-01-06 13:51 2.2K
chr16_random.axt.gz 2005-08-16 16:53 2.5K
chr10_random.axt.gz 2005-08-16 16:51 4.0K
chr5_random.axt.gz 2005-08-16 16:55 4.1K
chr19_random.axt.gz 2005-08-16 16:54 4.7K
chr12_random.axt.gz 2005-08-16 16:52 4.9K
chr22_random.axt.gz 2005-08-16 16:55 6.1K
chr13_random.axt.gz 2005-08-16 16:52 8.9K
chrM.axt.gz 2005-08-16 16:56 9.3K
chr3_random.axt.gz 2005-08-16 16:55 11K
chr8_random.axt.gz 2005-08-16 16:56 12K
chr2_random.axt.gz 2005-08-16 16:55 16K
chr4_random.axt.gz 2005-08-16 16:55 17K
chr7_random.axt.gz 2005-08-16 16:56 19K
chr9_random.axt.gz 2005-08-16 16:56 20K
chr6_random.axt.gz 2005-08-16 16:56 22K
chr15_random.axt.gz 2005-08-16 16:52 24K
chrX_random.axt.gz 2005-08-16 16:56 30K
chr17_random.axt.gz 2005-08-16 16:53 58K
chr1_random.axt.gz 2005-08-16 16:54 60K
chrY.axt.gz 2005-08-16 16:57 479K
chr21.axt.gz 2005-08-16 16:54 686K
chr22.axt.gz 2005-08-16 16:55 887K
chr20.axt.gz 2005-08-16 16:54 1.0M
chr18.axt.gz 2005-08-16 16:53 1.1M
chr15.axt.gz 2005-08-16 16:52 1.6M
chr16.axt.gz 2005-08-16 16:53 1.7M
chr14.axt.gz 2005-08-16 16:52 1.7M
chr13.axt.gz 2005-08-16 16:52 1.9M
chrX.axt.gz 2005-08-16 16:56 2.1M
chr17.axt.gz 2005-08-16 16:53 2.1M
chr9.axt.gz 2005-08-16 16:56 2.2M
chr10.axt.gz 2005-08-16 16:51 2.3M
chr8.axt.gz 2005-08-16 16:56 2.3M
chr19.axt.gz 2005-08-16 16:54 2.3M
chr12.axt.gz 2005-08-16 16:52 2.5M
chr11.axt.gz 2005-08-16 16:51 2.7M
chr6.axt.gz 2005-08-16 16:56 2.8M
chr7.axt.gz 2005-08-16 16:56 2.9M
chr5.axt.gz 2006-01-05 16:45 3.1M
chr3.axt.gz 2005-08-16 16:55 3.3M
chr4.axt.gz 2005-08-16 16:55 3.5M
chr2.axt.gz 2005-08-16 16:55 4.3M
chr1.axt.gz 2005-08-16 16:54 4.6M