This directory contains alignments of the human assembly (hg17, May 2004)
to the zebrafish assembly (danRer2, June 2004).
Files included in this directory:
- axtChrom directory: contains the axt alignments generated by blastz,
in one file per chromosome. Blastz output was converted to lav format,
which was then converted to axt format.
- humanHg17.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- humanHg17.net.gz: "net" file that describes rearrangements between the
species and the best human match to any part of the zebrafish genome.
The net format is described in
http://genome.ucsc.edu/goldenPath/help/net.html.
- md5sum.txt: checksums of the files in this directory
The alignments in the axtChrom directory are in "axt" format. For a
description, see http://genome.ucsc.edu/goldenPath/help/axt.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
species-specific repeats library for each genome. 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.
The axtNet alignments were processed with chainNet, netSyntenic,
and netClass 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/danRer2/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 available for public use.
The Zv4 zebrafish sequence data were produced by the Zebrafish Sequencing
Group at the Sanger Institute and can be obtained directly from
ftp://ftp.sanger.ac.uk/pub/zebrafish/. All sequence data are made available
before scientific publication with the understanding that the groups
involved in generating the data intend to publish the initial large-scale
analyses of the dataset. This will include a summary detailing the data that
have beeen generated and key features of the genome identified from genomic
assembly and clone mapping/sequencing. Any redistribution of the data
should carry this notice.
Name Last modified Size Description
Parent Directory -
axtChrom/ 2004-12-14 10:24 -
humanHg17.chain.gz 2004-12-21 15:06 28M
humanHg17.net.gz 2004-12-21 15:07 15M
md5sum.txt 2004-12-21 15:08 104