This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/tarSyr2/multiz20way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the tarsier genome (tarSyr2/WashU-2.0.1, Sep. 2013):
Assemblies used in these alignments: (alignment
type)
Tarsier - Tarsius syrichta
Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reference
Baboon - Papio anubis Mar. 2012 (Baylor Panu_2.0/papAnu2) syntenic
Bonobo - Pan paniscus May. 2012 (Max-Planck/panPan1) reciprocal best
Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) reciprocal best
Chimp - Pan troglodytes Feb. 2011 (CSAC 2.1.4/panTro4) syntenic
Crab-eating macaque - Macaca fascicularis
Jun. 2013 (WashU Macaca_fascicularis_5.0/macFas5) syntenic
Gibbon - Nomascus leucogenys Oct. 2012 (GGSC Nleu3.0/nomLeu3) syntenic
Golden snub-nosed monkey - Rhinopithecus roxellana
Oct. 2014 (Rrox_v1/rhiRox1) reciprocal best
Gorilla - Gorilla gorilla gorilla May 2011 (gorGor3.1/gorGor3) reciprocal best
Green monkey - Chlorocebus sabaeus
Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) syntenic
Human - Homo sapiens Dec. 2013 (GRCh38/hg38) syntenic
Marmoset - Callithrix jacchus Mar. 2009 (WUGSC 3.2/calJac3) syntenic
Mouse lemur - Microcebus murinus Jul. 2007 (Broad/micMur1) reciprocal best
Orangutan - Pongo pygmaeus abelii July 2007 (WUGSC 2.0.2/ponAbe2) syntenic
Proboscis monkey - Nasalis larvatus
Nov. 2014 (Charlie1.0/nasLar1) reciprocal best
Rhesus - Macaca mulatta Oct. 2010 (BGI CR_1.0/rheMac3) syntenic
Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) reciprocal best
Tree shrew - Tupaia belanger Dec. 2006 (Broad/tupBel1) reciprocal best
Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic
Dog - Canis lupus familiaris Sep. 2011 (Broad/canFam3) syntenic
---------------------------------------------------------------
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=tarSyr2&g=cons20way
based on the phylogenetic tree: tarSyr2.20way.nh
Files in this directory:
- tarSyr2.20way.nh - phylogenetic tree used during the multiz multiple alignment
- tarSyr2.20way.commonNames.nh - same as tarSyr2.20way.nh with the UCSC database
name replaced by the common name for the species
- tarSyr2.20way.scientificNames.nh - same as tarSyr2.20way.nh with the UCSC
database name replaced by the scientific name for the species
- upstream1000.xenoRefGene.maf.gz - alignments in regions upstream, see below
- upstream2000.xenoRefGene.maf.gz - alignments in regions upstream, see below
- upstream5000.xenoRefGene.maf.gz - alignments in regions upstream, see below
- tarSyr2.20way.maf.gz - alignments with gap annotation
- md5sum.txt - MD5 sum of the files to verify downloads
See also:
http://genomewiki.ucsc.edu/index.php/TarSyr2_20-way_conservation_alignment
The "alignments" directory contains compressed FASTA alignments
for the 'Xeno' RefSeq Gene CDS regions of the tarsier genome
(tarSyr2, Sep. 2013) aligned to the assemblies.
The tarSyr2.20way.maf.gz file contains the alignments to
the tarsier assembly, with additional annotations to
indicate gap context, and genomic breaks for the
sequence in the underlying genome assemblies. Beware, the compressed
data size of this file is 11 Gb, uncompressed is approximately 79 Gb.
The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for 'Xeno' 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
mouse, 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 the tarsier sequence; 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.
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/tarSyr2/phastCons20way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/tarSyr2/phyloP20way
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=tarSyr2&g=cons20way
---------------------------------------------------------------
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 11 Gb of compressed data in this directory,
The tarSyr2.20way.maf.gz file uncompresses to 79 Gb of data.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/tarSyr2/multiz20way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/tarSyr2/multiz20way
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 -
md5sum.txt 2015-04-17 15:50 434
upstream5000.xenoRefGene.maf.gz 2015-04-17 12:52 844M
upstream2000.xenoRefGene.maf.gz 2015-04-17 12:20 360M
upstream1000.xenoRefGene.maf.gz 2015-04-17 11:56 91M
alignments/ 2015-04-15 21:07 -
tarSyr2.20way.scientificNames.nh 2015-04-14 18:51 839
tarSyr2.20way.commonNames.nh 2015-04-14 18:51 683
tarSyr2.20way.nh 2015-04-14 18:51 687
tarSyr2.20way.maf.gz 2015-04-14 09:27 10G