This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/multiz11way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the X. tropicalis genome (xenTro9, Jul. 2016):
Assemblies used in these alignments:
- X. tropicalis Xenopus tropicalis Jul. 2016 DOE JGI v9.1/xenTro9
reference genome
- African clawed frog Xenopus laevis Aug. 2016 IXSC v2/xenLae2
- Tibetan frog Nanorana parkeri Mar. 2015 BGI ZX_2015/nanPar1
- Painted turtle Chrysemys picta bellii Mar. 2014 IPTGSC v3.0.3/chrPic2
- Chicken Gallus gallus May 2006 Gallus_gallus-5.0/galGal5
- Lizard Anolis carolinensis May 2010 anoCar2/Broad
- Opossum Monodelphis domestica Oct. 2006 Broad/monDom5
- Dog Canis lupus familiaris Sep. 2011 Broad CanFam3.1/canFam3
- Human Homo sapiens Dec. 2013 GRCh38/hg38
- Mouse Mus musculus Dec. 2011 GRCm38/mm10
- Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3
Syntenic net filtered MAF files used for multiz:
hg38, mm10, xenLae2, canFam3, monDom5, fr3, galGal5, anoCar2
Reciprocal best filtered MAF files used for multiz:
nanPar1 chrPic2
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro9&g=cons11way
based on the phylogenetic tree: xenTro9.11way.nh.
Files in this directory:
- xenTro9.11way.nh - phylogenetic tree used during the multiz multiple alignment
- xenTro9.11way.commonNames.nh - same as xenTro9.11way.nh with the UCSC database
names replaced by the common name for the species
- xenTro9.11way.scientificName.nh - same as xenTro9.11way.nh with the UCSC
database names replaced by the scientific name for the species
- xenTro9.11way.maf.gz - the multiple alignments on the
X. tropicalis reference genome
- upstream*.refGene.maf.gz - alignments of regions upstream of refGene genes
- md5sum.txt - md5 check sums of these files to verify correct download files
The xenTro9.11way.maf.gz file contain all the alignments for the chromosomes
in the X. tropicalis genome, including additional annotations to
indicate gap context and genomic breaks for the sequence in the underlying
genome assemblies. Note, the compressed data size of the
maf file is 853 Mb, uncompressed is 4.0 Gb.
The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the Xenopus genome (xenTro9, Jul. 2016)
aligned to the assemblies.
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro9&g=cons11way
based on the phylogenetic tree: xenTro9.11way.nh.
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/xenTro9/phastCons11way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/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 934 Mb of compressed data in this directory.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/multiz11way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/xenTro9/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.
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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 -
alignments/ 2017-05-02 16:48 -
md5sum.txt 2017-05-02 14:50 422
upstream1000.refGene.maf.gz 2017-05-02 14:38 5.3M
upstream2000.refGene.maf.gz 2017-05-02 14:39 8.8M
upstream5000.refGene.maf.gz 2017-05-02 14:40 21M
xenTro9.11way.commonNames.nh 2017-05-02 14:49 326
xenTro9.11way.maf.gz 2017-05-02 10:33 853M
xenTro9.11way.nh 2017-05-02 14:48 301
xenTro9.11way.scientificNames.nh 2017-05-02 14:49 418