This directory contains compressed multiple alignments of the following assemblies to the mouse genome (mm9, Mar. 2006): _ mouse Mus musculus July 2007, mm9 _ rat Rattus norvegicus Nov 2004, rn4 _ guinea pig Cavia porcellus Oct 2005, cavPor2 _ rabbit Oryctolagus cuniculus May 2005, oryCun1 _ human Homo sapiens Mar 2006, hg18 _ chimpanzee Pan troglodytes Mar 2006, panTro2 _ orangutan Pongo pygmaeus abelii July 2007, ponAbe2 _ rhesus Macaca mulatta Jan 2006, rheMac2 _ marmoset Callithrix jacchus June 2007, calJac1 _ bushbaby Otolemur garnetti Dec 2006, otoGar1 _ tree shrew Tupaia belangeri Dec 2006, tupBel1 _ shrew Sorex araneus June 2006, sorAra1 _ hedgehog Erinaceus europaeus June 2006, eriEur1 _ dog Canis familiaris May 2005, canFam2 _ cat Felis catus Mar 2006, felCat3 _ horse Equus caballus Jan 2007, equCab1 _ cow Bos taurus Aug 2006, bosTau3 _ armadillo Dasypus novemcinctus May 2005, dasNov1 _ elephant Loxodonta africana May 2005, loxAfr1 _ tenrec Echinops telfairi July 2005, echTel1 _ opossum Monodelphis domestica Jan 2006, monDom4 _ platypus Ornithorhychus anatinus Mar 2007, ornAna1 _ chicken Gallus gallus May 2006, galGal3 _ lizard Anolis carolinensis Feb 2007, anoCar1 _ frog Xenopus tropicalis Aug 2005, xenTro2 _ tetraodon Tetraodon nigroviridis Feb 2004, tetNig1 _ fugu Takifugu rubripes Oct 2004, fr2 _ stickleback Gasterosteus aculeatus Feb 2006, gasAcu1 _ medaka Oryzias latipes Apr 2006, oryLat1 _ zebrafish Danio rerio July 2007, danRer5 These alignments were prepared using the methods described in the track description file, multiz30way.html, based on the phylogenetic tree, 30way.nh. The maf/chr*.maf.gz files each contain all the alignments to that particular human chromosome. The multiz30wayAnno.tar.gz file contains the same alignments for all chromsomes, with additional annotations to indicate gap context, genomic breaks, and quality scores for the sequence in the underlying genome assemblies. The maf/upstream*.maf.gz files contain alignments in regions upstream of annotated transcription starts for RefSeq 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 mouse, 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 mouse; 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/mm9/phastCons30way --------------------------------------------------------------- To download a large file or multiple files from this directory, we recommend that you use ftp rather than downloading the files via our website. To do so: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/mm9/multiz30way 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 - 30way.nh 2007-10-03 10:35 1.1K alignments/ 2012-07-27 15:41 - maf/ 2019-11-06 11:05 - multiz30way.html 2007-11-15 05:53 22K