This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/multiz11way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the Gorilla genome (gorGor3, May 2011):
Assemblies used in these alignments:
Gorilla gorilla gorilla May 2011 Sanger gorGor3.1/gorGor3
Chimp Pan troglodytes Oct. 2010 CGSC 2.1.3/panTro3
Human Homo sapiens Feb. 2009 GRCh37/hg19
Gibbon Nomascus leucogenys Jan. 2010 GGSC Nleu1.0/nomLeu1
Orangutan Pongo pygmaeus abelii Jul. 2007 WUGSC 2.0.2/ponAbe2
Baboon Papio hamadryas Nov. 2008 Baylor 1.0/papHam1
Rhesus Macaca mulatta Jan. 2006 MGSC Merged 1.0/rheMac2
Marmoset Callithrix jacchus Mar. 2009 WUGSC 3.2/calJac3
Tarsier Tarsius syrichta Aug. 2008 Broad/tarSyr1
Mouse lemur Microcebus murinus Jun. 2003 Broad/micMur1
Bushbaby Otolemur garnettii Dec. 2006 Broad/otoGar1
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=gorGor3&g=cons11way
based on the phylogenetic tree: gorGor3.11way.nh.
Files in this directory:
- gorGor3.11way.nh - phylogenetic tree used during the
multiz multiple alignment
- gorGor3.commonNames.11way.nh - same as 11way.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 (gorGor3, May 2010)
aligned to the assemblies.
The multiz11way.maf.gz file contains all the alignments for all contigs
in the X. tropicalis 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
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/gorGor3/phastCons11way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/phyloP11way
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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 3.9 Gb of compressed data in this directory.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/multiz11way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/gorGor3/multiz11way
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 -
multiz11way.maf.gz 2011-12-06 09:47 3.9G
md5sum.txt 2011-12-08 13:37 212
maf/ 2019-11-06 10:58 -
gorGor3.commonNames.11way.nh 2011-12-08 11:19 290
gorGor3.11way.nh 2011-12-08 11:18 312
alignments/ 2011-12-09 09:53 -