This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz26way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the C. elegans genome (ce11, Feb. 2013):
Assemblies used in these alignments:
C. elegans Caenorhabditis elegans Feb. 2013 (WBcel235/ce11) reference
A. ceylanicum Ancylostoma ceylanicum Mar. 2014
(WS243/Acey_2013.11.30.genDNA/ancCey1)
Barber pole worm Haemonchus contortus Jul. 2013 (WormBase WS239/haeCon2)
C. angaria Caenorhabditis angaria Mar. 2012 (WS245/caeAng2)
C. brenneri Caenorhabditis brenneri Nov. 2010
(C. brenneri 6.0.1b/caePb3)
C. briggsae Caenorhabditis briggsae Apr. 2011 (WS225/cb4)
C. japonica Caenorhabditis japonica Aug. 2010 (WUSTL 7.0.1/caeJap4)
C. remanei Caenorhabditis remanei Jul. 2007 (WS220/caeRem4)
C. sp. 5 ju800 Caenorhabditis sp5 ju800 Jan. 2012
(WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51)
C. tropicalis Caenorhabditis tropicalis Nov. 2010 (WUSTL 3.0.1/caeSp111)
Dog heartworm Dirofilaria immitis Sep. 2013
(WS240/D. immitis v2.2/dirImm1)
Eye worm Loa loa Jul. 2012
(WS235/L_loa_Cameroon_isolate/loaLoa1)
Filarial worm Brugia malayi May. 2014
(WS244/B_malayi-3.1/bruMal2)
H. bacteriophora/m31e Heterorhabditis bacteriophora Aug. 2011
(WS229/H. bacteriophora 7.0/hetBac1)
M. hapla Meloidogyne hapla Sep. 2008
(M. hapla VW9 WS210/melHap1)
M. incognita Meloidogyne incognita Feb. 2008
(M. incognita WS245/PRJEA28837/melInc2)
Microworm Panagrellus redivivus Feb. 2013 (Pred3/panRed1)
N. americanus Necator americanus Dec. 2013
(WS242/N_americanus_v1/necAme1)
O. volvulus Onchocerca volvulus Nov. 2013
(WS241/O_volvulus_Cameroon_v3/oncVol1)
P. exspectatus Pristionchus exspectatus Mar. 2014
(WS243/P_exspectatus_v1/priExs1)
P. pacificus Pristionchus pacificus Aug. 2014 (P_pacificus-v2/priPac3)
Pig roundworm Ascaris suum Sep. 2012
(WS229/AscSuum_1.0/ascSuu1)
Pine wood nematode Bursaphelenchus xylophilus Nov. 2011
(WS229/B. xylophilus Ka4C1/burXyl1)
Threadworm Strongyloides ratti Sep. 2014 (S. ratti ED321/strRat2)
Trichinella Trichinella spiralis Jan. 2011
(WS225/Trichinella_spiralis-3.7.1/triSpi1)
Whipworm Trichuris suis Jul. 2014 (WS243/T. suis
DCEP-RM93M male/triSui1)
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce11&g=cons26way
based on the phylogenetic tree: ce11.26way.nh.
Files in this directory:
- ce11.26way.nh - phylogenetic tree used during the multiz multiple alignment
- ce11.26way.commonNames.nh - same as ce11.26way.nh with the UCSC database
names replaced by the common name for the species
- ce11.26way.scientificName.nh - same as ce11.26way.nh with the UCSC database
names replaced by the scientific name for the species
- upstream*.ensGene..maf.gz - alignments of regions upstream of Ensembl genes
- upstream*.refGene..maf.gz - alignments of regions upstream of RefSeq genes
- upstream*.ws245Genes..maf.gz - alignments of regions upstream of ws245 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 for three gene tracks, ws245Genes, refGene, ensGene,
of the C. elegans genome (ce11, Feb. 2013) 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 33 Mb, uncompressed is more than 2.4 Gb.
The .upstream*.*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl genes, RefSeq genes, and
the WormBase WS245 gene predictions, 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
C. elegans, 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/ce11/phastCons26way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP26way
---------------------------------------------------------------
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/ce11/multiz26way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/ce11/multiz26way
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 -
upstream5000.refGene.maf.gz 2015-09-09 11:34 471M
upstream2000.refGene.maf.gz 2015-09-09 11:15 193M
upstream5000.ensGene.maf.gz 2015-09-09 12:00 188M
upstream5000.ws245Genes.maf.gz 2015-09-08 17:13 188M
upstream1000.refGene.maf.gz 2015-09-09 10:51 84M
upstream2000.ensGene.maf.gz 2015-09-09 11:54 77M
upstream2000.ws245Genes.maf.gz 2015-09-08 17:07 77M
chrV.maf.gz 2015-08-13 14:42 63M
chrX.maf.gz 2015-08-13 14:42 58M
chrIV.maf.gz 2015-08-13 14:42 56M
chrI.maf.gz 2015-08-13 14:42 54M
chrII.maf.gz 2015-08-13 14:42 51M
chrIII.maf.gz 2015-08-13 14:42 51M
upstream1000.ensGene.maf.gz 2015-09-09 11:50 36M
upstream1000.ws245Genes.maf.gz 2015-09-08 17:03 35M
chrM.maf.gz 2015-08-13 14:41 137K
ce11.26way.scientificNames.nh 2015-09-08 14:15 1.2K
md5sum.txt 2015-09-09 12:35 1.0K
ce11.26way.commonNames.nh 2015-09-08 14:15 968
ce11.26way.nh 2015-09-08 14:15 869
alignments/ 2015-09-09 11:30 -