This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/ce10/multiz7way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the C. elegans genome (ce10, Oct. 2010):
Assemblies used in these alignments:
- C. elegans Oct. 2010 ce10/WS220
- C. briggsae Apr. 2011 cb4/WS225
- C. remanei July 2007 caeRem4/WS220
- C. sp. 11 ju1373 Nov. 2010 caeSp111/GCA_000186765.1
- C. brenneri Nov. 2010 caePb3/GCA_000143925.1
- C. japonica Aug. 2010 caeJap4/GCA_000147155.1
- C. angaria Oct. 2010 caeAng1/GCA_000165025.1/WS225
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce10&g=cons7way
based on the phylogenetic tree: ce10.7way.nh.
Files in this directory:
- ce10.7way.nh - phylogenetic tree used during the multiz multiple alignment
- ce10.commonNames.7way.nh - same as ce10.7way.nh with the UCSC database
names replaced by the common name for the species
- ensGene.upstream*.maf.gz - alignments of regions upstream of Ensembl genes
- chr*.maf.gz - the multiple alignments on C. elegans for each chromosome
- md5sum.txt - md5 check sums of these files to verify correct download files
The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the C. elegans genome (ce10, Oct. 2010)
aligned to the assemblies.
The chr*.maf.gz files contain all the alignments for the chromosomes
in the C. elegans 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 these
maf files is 198 Mb, uncompressed is more than 420 Mb.
The ensGene.upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for 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
human, 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 C. elegans; 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/ce10/phastCons7way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce10/phyloP7way
---------------------------------------------------------------
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/ce10/multiz7way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/ce10/multiz7way
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 2011-12-16 13:34 618
maf/ 2019-11-06 10:42 -
ensGene.upstream5000.maf.gz 2011-12-16 13:33 64M
ensGene.upstream2000.maf.gz 2011-12-16 13:32 20M
ensGene.upstream1000.maf.gz 2011-12-16 13:31 11M
chrX.maf.gz 2011-12-16 10:18 24M
chrV.maf.gz 2011-12-16 10:18 19M
chrM.maf.gz 2011-12-16 10:18 9.3K
chrIV.maf.gz 2011-12-16 10:18 15M
chrIII.maf.gz 2011-12-16 10:18 14M
chrII.maf.gz 2011-12-16 10:18 15M
chrI.maf.gz 2011-12-16 10:18 14M
ce10.commonNames.7way.nh 2011-12-16 13:26 200
ce10.7way.nh 2011-12-16 11:02 171