This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/rn5/multiz13way/README.txt
This directory contains compressed multiple alignments of the following
assemblies to the rat genome (rn5/RGSC 5.0, Mar. 2012):
Assemblies used in these alignments:
Rat Rattus norvegicus Mar 2012 RGSC 5.0/rn5 Reference species
Chicken Gallus gallus Nov 2011 ICGSC Gallus_gallus-4.0/galGal4 Net
Chimp Pan troglodytes Feb 2011 CSAC 2.1.4/panTro4 Syntenic net
Cow Bos taurus Oct 2011 Baylor Btau_4.6.1/bosTau7 Syntenic net
Dog Canis lupus familiaris Sep 2011 Broad CanFam3.1/canFam3 Syntenic net
Guinea pig Cavia porcellus Feb 2008 Broad/cavPor3 Syntenic net
Human Homo sapiens Dec 2013 GRCh38/hg38 Syntenic net
Mouse Mus musculus Dec 2011 GRCm38/mm10 Syntenic net
Opossum Monodelphis domestica Oct 2006 Broad/monDom5 Net
Panda Ailuropoda melanoleuca Dec 2009 BGI-Shenzhen 1.0/ailMel1 Reciprocal best
Rhesus Macaca mulatta Oct 2010 BGI CR_1.0/rheMac3 Syntenic net
Turkey Meleagris gallopavo Dec 2009 TGC Turkey_2.01/melGal1 Net
Zebrafish Danio rerio Jul 2010 Zv9/danRer7 Net
---------------------------------------------------------------
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rn5&g=cons13way
based on the phylogenetic tree: rn5.13way.nh.
Files in this directory:
- rn5.13way.nh - phylogenetic tree used during the multiz multiple alignment
- rn5.13way.commonNames.nh - same as rn5.13way.nh with the UCSC database
name replaced by the common name for the species
- rn5.13way.scientificNames.nh - same as rn5.13way.nh with the UCSC
database name replaced by the scientific name for the species
See also:
http://genomewiki.ucsc.edu/index.php/rn5_13way_conservation_alignment
http://genomewiki.ucsc.edu/index.php/Rn5_13-way_Genome_size_statistics
http://genomewiki.ucsc.edu/index.php/Rn5_13-way_conservation_lastz_parameters
The "alignments" directory contains compressed FASTA alignments
for the Ensembl CDS regions of the rat genome (rn5/RGSC 5.0, Mar. 2012)
aligned to the assemblies.
The maf/chr*.maf.gz files each contain all the alignments to that particular
rat chromosome, with additional annotations to indicate gap context, and
genomic breaks for the sequence in the underlying genome assemblies. Beware,
the compressed data size of these files is about 4.3 Gb, uncompressed
size is about 54 Gb.
The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl 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
rat, 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 rat; 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/rn5/phastCons13way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/rn5/phyloP13way
---------------------------------------------------------------
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 -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/multiz13way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/rn5/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.
---------------------------------------------------------------
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/ 2014-05-08 14:31 -
maf/ 2019-11-06 11:15 -
md5sum.txt 2014-05-09 15:11 331
rn5.13way.commonNames.nh 2014-05-09 15:07 374
rn5.13way.nh 2014-05-09 15:00 397
rn5.13way.scientificNames.nh 2014-05-09 15:07 503
upstream1000.maf.gz 2014-05-08 14:35 49
upstream2000.maf.gz 2014-05-08 14:35 49
upstream5000.maf.gz 2014-05-08 14:35 49