This directory contains compressed multiple alignments of the following assemblies to the Cow genome (bosTau4, Oct 2007): - cow Bos taurus Oct 2007, bosTau4 reference - dog Canis familiaris May 2005, canFam2 syntenic net - human Homo sapiens Mar 2006, hg18 syntenic net - mouse Mus musculus July 2007, mm9 syntenic net - platypus Ornithorhychus anatinus Mar 2007, ornAna1 syntenic net These alignments were prepared using the methods described in the track description file, multiz5way.html, based on the phylogenetic tree, 5way.nh. The bosTau4.5way.maf.gz file contains all the alignments to the Cow chromosomes and chrUn contigs, with additional annotations to indicate gap context. The maf/upstream*.maf.gz files contain alignments in regions upstream of annotated transcription starts for MGC 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 cow, 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 cow; 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/bosTau4/phastCons5way --------------------------------------------------------------- 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/bosTau4/multiz5way 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.