This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/multiz13way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the Marmoset genome (calJac3, March 2009):
- marmoset Callithrix jacchus Mar 2009, calJac3 reference
- human Homo sapiens Feb 2009, hg19 chain nboon
- Baboon Papio hamadryas Nov 2008, papHam1 recip best
- Bushbaby Otolemur garnettii Dec 2006, otoGar1 recip best
- Chimp Pan troglodytes Mar 2006, panTro2 chain net
- Dog Canis lupus familiaris May 2005, canFam2 chain net
- Gorilla Gorilla gorilla gorilla Oct 2009, gorGor2 recip best
- Mouse Mus musculus July 2007, mm9 chain net
- Opossum Monodelphis domestica Oct 2006, monDom5 chain net
- Orangutan Pongo pygmaeus abelii July 2007, ponAbe2 chain net
- Rhesus Macaca mulatta Jan 2006, rheMac2 chain net
- Mouse lemur Microcebus murinus Jun 2003, micMur1 recip best
- Tarsier Tarsier syrichta Aug 2008, tarSyr1 recip best
These alignments were prepared using the methods described in the
track description file, multiz13way.html, based on the
phylogenetic tree, 13way.nh.
The calJac3.13way.maf.gz file contains all the alignments to the
Marmoset contigs, with additional annotations to indicate gap context.
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
marmoset, 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 marmoset; 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/calJac3/phastCons13way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phyloP13way
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=calJac3&g=cons13way
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To download a large file or multiple files from this directory, we recommend
that you use ftp rather than downloading the files via our website. To do so:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/calJac3/multiz13way
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/ 2011-06-13 16:27 -
maf/ 2019-11-06 10:40 -
13way.nh 2011-04-29 14:06 121
commonNames.13way.nh 2011-04-29 14:06 125
md5sum.txt 2011-04-29 14:17 405
upstream1000.maf.gz 2011-04-22 14:03 71M
upstream2000.maf.gz 2011-04-22 14:41 160M
upstream5000.maf.gz 2011-04-22 15:15 640M
calJac3.13way.maf.gz 2011-04-21 09:40 5.3G