This directory contains alignments of the Fugu assembly
(fr1, Aug. 2002) to the zebrafish assembly (danRer1, Nov. 2003)
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 -114 -31 -123
C -114 100 -125 -31
G -31 -125 100 -114
T -123 -31 -114 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 3000 for the first pass
and 3000 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.
The .lav format blastz output, which does not include the sequence, was
converted to .axt with lavToAxt.
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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/danRer1/fr1/. 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 Zv3 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 -
md5sum.txt 2004-07-20 21:19 1.3K
chrUn.axt.gz 2004-06-13 22:36 74M
chrNA.axt.gz 2004-06-13 22:33 67M
chr22.axt.gz 2004-06-13 22:32 13M
chrFinished.axt.gz 2004-06-13 22:32 8.8M
chr4.axt.gz 2004-06-13 22:32 7.7M
chr8.axt.gz 2004-06-13 22:31 5.4M
chr3.axt.gz 2004-06-13 22:31 7.5M
chr23.axt.gz 2004-06-13 22:31 4.9M
chr7.axt.gz 2004-06-13 22:31 5.3M
chr20.axt.gz 2004-06-13 22:31 3.9M
chr2.axt.gz 2004-06-13 22:31 3.9M
chr6.axt.gz 2004-06-13 22:31 3.8M
chr19.axt.gz 2004-06-13 22:31 3.6M
chr9.axt.gz 2004-06-13 22:31 3.1M
chr21.axt.gz 2004-06-13 22:31 2.5M
chr25.axt.gz 2004-06-13 22:30 1.8M
chr5.axt.gz 2004-06-13 22:30 5.1M
chr24.axt.gz 2004-06-13 22:30 2.7M
chrM.axt.gz 2004-06-13 22:29 3.7K
chr17.axt.gz 2004-06-13 22:22 5.8M
chr15.axt.gz 2004-06-13 22:22 7.3M
chr1.axt.gz 2004-06-13 22:22 5.1M
chr18.axt.gz 2004-06-13 22:22 3.4M
chr11.axt.gz 2004-06-13 22:22 3.1M
chr10.axt.gz 2004-06-13 22:22 4.3M
chr12.axt.gz 2004-06-13 22:22 3.0M
chr13.axt.gz 2004-06-13 22:21 2.2M
chr14.axt.gz 2004-06-13 22:20 5.5M
chr16.axt.gz 2004-06-13 22:20 3.9M