This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/galVar1/multiz5way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the Guinea pig genome (galVar1, Jun. 2014):
Assemblies used in these alignments:
Malayan flying lemur Galeopterus variegatus Jun. 2014 (G_variegatus-3.0.2/galVar1) reference
Guinea pig Cavia porcellus Feb. 2008 (Broad/cavPor3) reference
Mouse Mus musculus Dec. 2011 (GRCm38/mm10)
Human Homo sapiens Dec. 2013 (GRCh38/hg38)
Tree shrew Tupaia belangeri Dec. 2006 (Broad/tupBel1)
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=galVar1&g=cons5way
based on the phylogenetic tree: galVar1.5way.nh.
Files in this directory:
- galVar1.5way.nh - phylogenetic tree used during the multiz multiple alignment
- galVar1.5way.commonNames.nh - same as galVar1.5way.nh with the UCSC database
names replaced by the common name for the species
- galVar1.5way.scientificName.nh - same as galVar1.5way.nh with the UCSC database
names replaced by the scientific name for the species
- upstream*.ncbiRefSeq..maf.gz - alignments of regions upstream of Ensembl genes
- galVar1.5way.maf.gz - the multiple alignments on the Guinea pig genome
- md5sum.txt - md5 check sums of these files to verify correct download files
The "alignments" directory contains compressed FASTA alignments
for the CDS regions for the gene track ncbiRefSeq (June 2015 version)
of the Guinea pig genome (galVar1, Jun. 2014) aligned to the assemblies.
The galVar1.5way.maf.gz file contain all the alignments for the chromosomes
in the Guinea pig 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 3.0 Gb, uncompressed is more than 13 Gb.
The .upstream*.*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for version 81/July 2015 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
Guinea pig 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 Guinea pig 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/galVar1/phastCons5way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/galVar1/phyloP5way
---------------------------------------------------------------
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 240 Mb of compressed data in this directory.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/galVar1/multiz5way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/galVar1/multiz5way
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/ 2016-08-15 09:59 -
md5sum.txt 2016-05-11 12:36 472
upstream5000.ncbiRefSeq.maf.gz 2016-05-11 11:54 68M
upstream2000.ncbiRefSeq.maf.gz 2016-05-11 11:48 30M
upstream1000.ncbiRefSeq.maf.gz 2016-05-11 11:42 16M
galVar1.5way.scientificNames.nh 2016-05-09 15:15 170
galVar1.5way.commonNames.nh 2016-05-09 15:14 143
galVar1.5way.nh 2016-05-09 15:14 126
galVar1.5way.maf.gz 2016-05-04 10:33 2.9G