This directory contains zipped multiple alignments of the zebrafish genome
(danRer4, Mar. 2006) to the following assemblies:
- Fugu (fr1, Aug. 2002)
- Tetraodon (tetNig1, Feb. 2004)
- X. tropicalis (xenTro2, Aug. 2005)
- Opossum (monDom4, Jan. 2006)
- Mouse (mm8, Feb. 2006)
- Human (hg18, Mar. 2006)
The chr*.maf.gz files each contain all the alignments to that
particular zebrafish chromosome.
The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for RefSeq genes with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in
zebrafish, whether or not alignments actually exist. In situations where no
alignments exist or the alignments of one or more species are missing,
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in zebrafish; therefore, only the
species name is displayed in the alignment data and no position information
is recorded. The alignment score is always zero in these files. These files
are updated weekly.
For a description of the multiple alignment format (MAF),
see http://genome.ucsc.edu/goldenPath/help/maf.html.
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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/danRer4/multiz7way/. 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.
For data restrictions regarding the aligned genomes, see
http://genome.ucsc.edu/goldenPath/credits.html.
Name Last modified Size Description
Parent Directory -
maf/ 2019-11-06 10:46 -
md5sum.txt 2008-10-16 12:18 1.3K
chrUn_random.maf.gz 2006-05-29 13:03 10M
chrNA_random.maf.gz 2006-05-29 13:02 39M
chrM.maf.gz 2006-05-29 13:02 32K
chr9.maf.gz 2006-05-29 13:02 23M
chr8.maf.gz 2006-05-29 13:02 26M
chr7.maf.gz 2006-05-29 13:01 34M
chr6.maf.gz 2006-05-29 13:01 28M
chr5.maf.gz 2006-05-29 13:01 33M
chr4.maf.gz 2006-05-29 13:00 17M
chr3.maf.gz 2006-05-29 13:00 29M
chr25.maf.gz 2006-05-29 13:00 16M
chr24.maf.gz 2006-05-29 13:00 18M
chr23.maf.gz 2006-05-29 12:59 21M
chr22.maf.gz 2006-05-29 12:59 17M
chr21.maf.gz 2006-05-29 12:59 22M
chr20.maf.gz 2006-05-29 12:59 24M
chr2.maf.gz 2006-05-29 12:58 25M
chr19.maf.gz 2006-05-29 12:58 20M
chr18.maf.gz 2006-05-29 12:58 22M
chr17.maf.gz 2006-05-29 12:58 27M
chr16.maf.gz 2006-05-29 12:57 25M
chr15.maf.gz 2006-05-29 12:57 22M
chr14.maf.gz 2006-05-29 12:57 32M
chr13.maf.gz 2006-05-29 12:56 26M
chr12.maf.gz 2006-05-29 12:56 23M
chr11.maf.gz 2006-05-29 12:56 20M
chr10.maf.gz 2006-05-29 12:56 22M
chr1.maf.gz 2006-05-29 12:55 27M