This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/ce9/multiz10way/README.txt This directory contains compressed multiple alignments of the following assemblies to the C. elegans genome (ce9/WS210, Jan. 2010): Assemblies used in these alignments: - Caenorhabditis elegans Jan. 2010 ce9/WS210 - Caenorhabditis briggsae Jan. 2007 cb3/WS210/WUGSC 1.0 - Caenorhabditis remanei May 2007 caeRem3/WS210/WUGSC 15.0.1 - Caenorhabditis brenneri Feb. 2008 caePb2/WS210/WUGSC 6.0.1 - Caenorhabditis japonica Sep. 2010 caeJap3/WUGSC 7.0.1 - Haemonchus contortus Dec. 2009 haeCon1/WS210 - Pristionchus pacificus Dec. 2008 priPac2/WUGSC 5.0.1 - Meloidogyne hapla VW9 Sep. 2008 melHap1/WS210 - Meloidogyne incognita Feb. 2008 melInc1/WS210 - Brugia malayi Sep. 2007 bruMal1/WS210/TIGR 1.0 These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce9&g=cons10way based on the phylogenetic tree: 10way.nh. Files in this directory: - 10way.nh - phylogenetic tree used during the multiz multiple alignment - commonNames.10way.nh - same as 10way.nh with the UCSC database name replaced by the common name for the species The "alignments" directory contains compressed FASTA alignments for the CDS regions of the C. elegans genome (ce9/WS210, Jan. 2010) aligned to the assemblies. The maf/chr*.maf.gz files each contain all the alignments to that particular C. elegans chromosome, with additional annotations to indicate gap context and genomic breaks. The sangerGene.upstream*.maf.gz files contain alignments in regions upstream of annotated transcription starts for the WormBase/Sanger 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 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. 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/ce9/phastCons10way/ PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/ce9/phyloP10way/ --------------------------------------------------------------- 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. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/ce9/multiz10way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/ce9/multiz10way To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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. ------------------------------------------------------------------------