This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the X. tropicalis genome (xenTro3, Nov 2009):
Assemblies used in these alignments:
- X. tropicalis Xenopus tropicalis Nov. 2009 xenTro3/JGI 4.2
- Lizard Anolis carolinensis May 2010 anoCar2/Broad
- Chicken Gallus gallus May 2006 galGal3/WUGSC 2.1
- Turkey Meleagris gallopavo Dec. 2009 melGal1/TGC Turkey_2.01
- Opossum Monodelphis domestica Oct. 2006 monDom5/Broad
- Rat Rattus norvegicus Nov. 2004 rn4/Baylor 3.4
- Mouse Mus musculus Jul. 2007 mm9/NCBI37
- Human Homo sapiens Feb. 2009 hg19/GRCh37
- Zebrafish Danio rerio Jul. 2010 danRer7/Zv9
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro3&g=cons9way
based on the phylogenetic tree: 9way.nh.
Files in this directory:
- 9way.nh - phylogenetic tree used during the multiz multiple alignment
- xenTro3.commonNames.9way.nh - same as 9way.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 (xenTro3, May 2010)
aligned to the assemblies.
The multiz9way.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 3 Gb. (664 Mb 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/xenTro3/phastCons9way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phyloP9way
---------------------------------------------------------------
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 -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/xenTro3/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.
---------------------------------------------------------------
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 11:19 -
md5sum.txt 2011-10-04 11:23 387
upstream5000.ensGene.maf.gz 2011-10-04 11:17 59M
upstream2000.ensGene.maf.gz 2011-10-04 11:11 22M
upstream1000.ensGene.maf.gz 2011-10-04 11:05 13M
alignments/ 2011-09-30 17:20 -
xenTro3.commonNames.9way.nh 2011-09-29 15:28 230
9way.nh 2011-09-29 15:27 225
multiz9way.maf.gz 2011-09-28 14:14 663M