This directory contains compressed multiple alignments of the following assemblies to the Lancelet genome (braFlo1, Mar 2006): - lancelet Branchiostoma floridae Mar 2006, braFlo1 reference - human Homo sapiens Mar 2006, hg18 recip best net - mouse Mus musculus July 2007, mm9 recip best net - chicken Gallus gallus May 2006, galGal3 recip best net - lamprey Petromyzon marinus June 2007, petMar1 recip best net These alignments were prepared using the methods described in the track description file, multiz5way.html, based on the phylogenetic tree, 5way.nh. The braFlo1.5way.maf.gz file contains all the alignments to the Lancelet contigs, with additional annotations to indicate gap context. The maf/upstream*.maf.gz files contain alignments in regions upstream of annotated transcription starts for Xeno 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 lancelet, 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 lancelet; 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/braFlo1/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/braFlo1/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. Checksum values for all files in this directory can be found in md5sum.txt.