This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the Fugu genome (fr3, Oct. 2011):
Assemblies used in these alignments:
Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3
Tetraodon Tetraodon nigroviridis Mar. 2007 Genoscope 8.0/tetNig2
Nile tilapia Oreochromis niloticus Jan. 2011 Broad/oreNil1
Stickleback Gasterosteus aculeatus Feb. 2006 Broad/gasAcu1
Atlantic cod Gadus morhua May. 2010 Genofisk/gadMor1
Medaka Oryzias latipes Oct. 2005 NIG/oryLat2
Zebrafish Danio rerio Jul. 2010 Zv9/danRer7
Coelacanth Latimeria chalumnae Aug. 2011 Broad/latCha1
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=fr3&g=cons8way
based on the phylogenetic tree: fr3.8way.nh.
Files in this directory:
- fr3.8way.nh - phylogenetic tree used during the
multiz multiple alignment
- fr3.commonNames.8way.nh - same as 8way.nh with the UCSC database
names replaced by the common name for the species
The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the zebrafish genome (fr3, Oct. 2011)
aligned to the assemblies.
The multiz8way.maf.gz file contains all the alignments for all contigs
in the Fugu genome. Additional annotations to indicate gap
context and genomic breaks for the sequence in the underlying genome
assemblies. Beware, the uncompressed
data size of this file is 28 Gb. (3.8 Gb compressed)
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
fugu, 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 fugu; 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/fr3/phastCons8way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/fr3/phyloP8way
---------------------------------------------------------------
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 3.0 Gb of compressed data in this directory.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/fr3/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 -
multiz8way.maf.gz 2012-02-21 13:55 705M
fr3.commonNames.8way.nh 2012-02-23 13:25 222
md5sum.txt 2012-02-23 13:38 201
fr3.8way.nh 2012-02-23 13:25 201
maf/ 2019-11-06 10:54 -
alignments/ 2012-02-23 15:02 -