This directory contains compressed multiple alignments of the following assemblies to the human genome (hg18, Mar. 2006): _ human Homo sapiens Mar 2006, hg18 _ chimpanzee Pan troglodytes Mar 2006, panTro2 _ rhesus Macaca mulatta Jan 2006, rheMac2 _ bushbaby Otolemur garnetti Dec 2006, otoGar1 _ tree shrew Tupaia belangeri Dec 2006, tupBel1 _ mouse Mus musculus Feb 2006, mm8 _ rat Rattus norvegicus Nov 2004, rn4 _ guinea pig Cavia porcellus Oct 2005, cavPor2 _ rabbit Oryctolagus cuniculus May 2005, oryCun1 _ 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 Feb 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 _ lizard Anolis carolinensis Feb 2007, anoCar1 _ chicken Gallus gallus May 2006, galGal3 _ frog Xenopus tropicalis Aug 2005, xenTro2 _ fugu Takifugu rubripes Oct 2004, fr2 _ tetraodon Tetraodon nigroviridis Feb 2004, tetNig1 _ stickleback Gasterosteus aculeatus Feb 2006, gasAcu1 _ medaka Oryzias latipes Apr 2006, oryLat1 _ zebrafish Danio rerio Mar 2006, danRer4 These alignments were prepared using the methods described in the track description file, multiz28way.html, based on the phylogenetic tree, 28way.nh. The maf/chr*.maf.gz files each contain all the alignments to that particular human chromosome. The multiz28wayAnno.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 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 human; 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/hg18/phastCons28way --------------------------------------------------------------- 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/hg18/multiz28way 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 - multiz28wayAnno.tar.gz 2007-05-31 11:42 15G multiz28way.html 2007-06-25 14:04 20K 28way.nh 2007-06-05 12:00 468 maf/ 2021-08-03 19:33 - alignments/ 2011-02-23 17:23 -