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 - ce10.7way.nh 2011-12-16 11:02 171 ce10.commonNames.7way.nh 2011-12-16 13:26 200 chrI.maf.gz 2011-12-16 10:18 14M chrII.maf.gz 2011-12-16 10:18 15M chrIII.maf.gz 2011-12-16 10:18 14M chrIV.maf.gz 2011-12-16 10:18 15M chrM.maf.gz 2011-12-16 10:18 9.3K chrV.maf.gz 2011-12-16 10:18 19M chrX.maf.gz 2011-12-16 10:18 24M ensGene.upstream1000.maf.gz 2011-12-16 13:31 11M ensGene.upstream2000.maf.gz 2011-12-16 13:32 20M ensGene.upstream5000.maf.gz 2011-12-16 13:33 64M maf/ 2019-11-06 10:42 - md5sum.txt 2011-12-16 13:34 618