This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/multiz8way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the zebrafish genome (danRer7, Jul. 2010):
Assemblies used in these alignments:
- Human Homo sapiens Feb. 2009 hg19/GRCh37
- Mouse Mus musculus July 2007 mm9
- X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
- Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
- Fugu Takifugu rubripes Oct. 2004 fr2
- Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
- Medaka Oryzias latipes Oct. 2005 oryLat2
- Zebrafish Danio rerio Jul. 2010 danRer7
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer7&g=cons8way
based on the phylogenetic tree: 8way.nh.
Files in this directory:
- 8way.nh - phylogenetic tree used during the multiz multiple alignment
- commonNames.8way.nh - same as 8way.nh with the UCSC database name
replaced by the common name for the species
The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the zebrafish genome (danRer7, Jul. 2010)
aligned to the assemblies.
The multiz8way.maf.gz file contains all the alignments for all chromosomes
and contigs in the zebrafish genome.
Additional annotations to indicate gap context, genomic breaks,
and quality scores for the
sequence in the underlying genome assemblies. Beware, the compressed
data size of this file is 850 Mb, uncompressed is more than 3.2 Gb.
The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl 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
human, 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 human; 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 multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.
PhastCons conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/phastCons8way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/phyloP8way
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To download a large file or multiple files from this directory, we recommend
that you use rsync or ftp rather than downloading the files via our website.
There is approximately 31 Gb of compressed data in this directory.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer7/multiz8way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/danRer7/multiz8way
To download multiple files from the UNIX command line, use the "mget" command.
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Use the "prompt" command to toggle the interactive mode if you do not want
to be prompted for each file that you download.
---------------------------------------------------------------
All the files in this directory are freely usable for any
purpose. For data use restrictions regarding the individual
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.
Name Last modified Size Description
Parent Directory -
upstream5000.ensGene.maf.gz 2011-10-04 11:56 164M
upstream2000.ensGene.maf.gz 2011-10-04 11:32 50M
upstream1000.ensGene.maf.gz 2011-10-04 11:09 30M
multiz8way.maf.gz 2011-05-12 09:45 801M
md5sum.txt 2011-10-04 13:01 379
maf/ 2019-11-06 10:47 -
commonNames.8way.nh 2011-01-04 16:10 210
8way.nh 2010-12-22 10:12 194