This directory contains compressed FASTA alignments for the CDS regions of the human genome (hg18, Mar. 2006) aligned to the following assemblies: _ Human Homo sapiens Mar. 2006 hg18 _ Chimp Pan troglodytes Mar. 2006 panTro2 _ Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1 _ Orangutan Pongo pygmaeus abelii July 2007 ponAbe2 _ Rhesus Macaca mulatta Jan. 2006 rheMac2 _ Marmoset Callithrix jacchus June 2007 calJac1 _ Tarsier Tarsius syrichta Aug. 2008 tarSyr1 _ Mouse lemur Microcebus murinus Jun. 2003 micMur1 _ Bushbaby Otolemur garnettii Dec. 2006 otoGar1 _ TreeShrew Tupaia belangeri Dec. 2006 tupBel1 _ Mouse Mus musculus July 2007 mm9 _ Rat Rattus norvegicus Nov. 2004 rn4 _ Kangaroo rat Dipodomys ordii July 2008 dipOrd1 _ Guinea Pig Cavia porcellus Feb. 2008 cavPor3 _ Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1 _ Rabbit Oryctolagus cuniculus May 2005 oryCun1 _ Pika Ochotona princeps July 2008 ochPri2 _ Alpaca Vicugna pacos July 2008 vicPac1 _ Dolphin Tursiops truncatus Feb. 2008 turTru1 _ Cow Bos taurus Oct. 2007 bosTau4 _ Horse Equus caballus Sep. 2007 equCab2 _ Cat Felis catus Mar. 2006 felCat3 _ Dog Canis lupus familiaris May 2005 canFam2 _ Microbat Myotis lucifugus Mar. 2006 myoLuc1 _ Megabat Pteropus vampyrus July 2008 pteVam1 _ Hedgehog Erinaceus europaeus June 2006 eriEur1 _ Shrew Sorex araneus June 2006 sorAra1 _ Elephant Loxodonta africana July 2008 loxAfr2 _ Rock hyrax Procavia capensis July 2008 proCap1 _ Tenrec Echinops telfairi July 2005 echTel1 _ Armadillo Dasypus novemcinctus July 2008 dasNov2 _ Sloth Choloepus hoffmanni July 2008 choHof1 _ Opossum Monodelphis domestica Jan. 2006 monDom4 _ Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1 _ Chicken Gallus gallus May 2006 galGal3 _ Zebra finch Taeniopygia guttata July 2008 taeGut1 _ Lizard Anolis carolinensis Feb. 2007 anoCar1 _ X. tropicalis 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 Oct. 2005 oryLat2 _ Zebrafish Danio rerio July 2007 danRer5 _ Lamprey Petromyzon marinus Mar. 2007 petMar1 Files included in this directory: - knownGene.exon*.fa.gz: for each exon in the hg18 UCSC Gene track, this file contains either amino acids (AA) or nucleotides (Nuc) for hg18 and the aligning genomes. - knownCanonical.exon*.fa.gz: for each exon in the hg18 canonical set of UCSC Genes, this file contains either amino acids (AA) or nucleotides (Nuc) for hg18 and the aligning genomes. - refGene.exon*.fa.gz: for each exon in the hg18 RefSeq Gene track, this file contains either amino acids (AA) or nucleotides (Nuc) for hg18 and the aligning genomes. For a description of multiple alignment format (MAF), see http://genome.ucsc.edu/goldenPath/help/maf.html and http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA. --------------------------------------------------------------- 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: go to the directory goldenPath/hg18/multiz44way/alignments 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.