This directory contains zipped multiple alignments of the zebrafish genome
(danRer3, May 2005) to the following assemblies:
- Tetraodon (tetNig1, Feb. 2004)
- Fugu (fr1, Aug. 2002)
- Human (hg18, Feb. 2006)
- Mouse (mm7, Aug. 2005)
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.
-------------------------------------------------------------------
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/danRer3/multiz5way/. 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 -
chr12.maf.gz 2006-02-06 08:14 4.9M
chr11.maf.gz 2006-02-06 08:14 5.4M
chr10.maf.gz 2006-02-06 08:14 6.0M
chr15.maf.gz 2006-02-06 08:14 6.5M
chr16.maf.gz 2006-02-06 08:15 7.3M
chr13.maf.gz 2006-02-06 08:15 6.8M
chr18.maf.gz 2006-02-06 08:15 7.0M
chr17.maf.gz 2006-02-06 08:15 6.9M
chr1.maf.gz 2006-02-06 08:15 7.7M
chr14.maf.gz 2006-02-06 08:15 9.4M
chrM.maf.gz 2006-02-06 08:15 21K
chr25.maf.gz 2006-02-06 08:16 3.8M
chr4.maf.gz 2006-02-06 08:17 5.0M
chr6.maf.gz 2006-02-06 08:17 4.8M
chr24.maf.gz 2006-02-06 08:17 4.8M
chr21.maf.gz 2006-02-06 08:17 5.5M
chr22.maf.gz 2006-02-06 08:17 6.4M
chr8.maf.gz 2006-02-06 08:17 5.8M
chr2.maf.gz 2006-02-06 08:17 7.0M
chr9.maf.gz 2006-02-06 08:17 6.2M
chr3.maf.gz 2006-02-06 08:17 7.1M
chr23.maf.gz 2006-02-06 08:17 7.5M
chr20.maf.gz 2006-02-06 08:17 7.5M
chr7.maf.gz 2006-02-06 08:18 8.5M
chr19.maf.gz 2006-02-06 08:18 9.3M
chr5.maf.gz 2006-02-06 08:18 11M
chrUn.maf.gz 2006-02-06 08:22 24M
chrNA.maf.gz 2006-02-06 08:24 31M
md5sum.txt 2006-02-22 10:03 1.3K
maf/ 2019-11-06 10:46 -