This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/monDom5/multiz9way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the opossum genome (monDom5, Oct. 2006):
_ Opossum Monodelphis domestica Oct. 2006 monDom5
_ Wallaby Macropus eugenii Nov. 2007 macEug1
_ Human Homo sapiens Mar. 2006 hg18
_ Mouse Mus musculus July 2007 mm9
_ Dog Canis lupus familiaris May 2005 canFam2
_ Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
_ Chicken Gallus gallus May 2006 galGal3
_ X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
_ Zebrafish Danio rerio July 2007 danRer5
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=monDom5&g=multiz9way
based on the phylogenetic tree: 9way.nh.
Files in this directory:
- 9way.nh - phylogenetic tree for the phastCons calculations
The maf/chr*.maf.gz files each contain all the alignments to that
particular opossum chromosome, with additional annotations to
indicate gap context, genomic breaks, and quality scores for the
sequence in the underlying genome assemblies.
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
opossum, 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 opossum; 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/hg18/phastCons9way
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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 5.8 Gb of compressed data in this directory.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom5/multi9way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/monDom5/multiz9way
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.
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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 -
maf/ 2019-11-06 11:06 -
9way.nh 2009-01-08 14:30 81