This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/README.txt This directory contains compressed multiple alignments of the following assemblies to the Fugu genome (fr3, Oct. 2011): Assemblies used in these alignments: Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3 Tetraodon Tetraodon nigroviridis Mar. 2007 Genoscope 8.0/tetNig2 Nile tilapia Oreochromis niloticus Jan. 2011 Broad/oreNil1 Stickleback Gasterosteus aculeatus Feb. 2006 Broad/gasAcu1 Atlantic cod Gadus morhua May. 2010 Genofisk/gadMor1 Medaka Oryzias latipes Oct. 2005 NIG/oryLat2 Zebrafish Danio rerio Jul. 2010 Zv9/danRer7 Coelacanth Latimeria chalumnae Aug. 2011 Broad/latCha1 These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=fr3&g=cons8way based on the phylogenetic tree: fr3.8way.nh. Files in this directory: - fr3.8way.nh - phylogenetic tree used during the multiz multiple alignment - fr3.commonNames.8way.nh - same as 8way.nh with the UCSC database names replaced by the common name for the species The "alignments" directory contains compressed FASTA alignments for the CDS regions of the zebrafish genome (fr3, Oct. 2011) aligned to the assemblies. The multiz8way.maf.gz file contains all the alignments for all contigs in the Fugu genome. Additional annotations to indicate gap context and genomic breaks for the sequence in the underlying genome assemblies. Beware, the uncompressed data size of this file is 28 Gb. (3.8 Gb compressed) The upstream*.maf.gz files contain alignments in regions upstream of annotated transcription starts for Ensembl 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 fugu, 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 fugu; 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/fr3/phastCons8way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/fr3/phyloP8way --------------------------------------------------------------- To download a large file or multiple files from this directory, we recommend that you use rsync or ftp rather than downloading the files via our website. There is approximately 3.0 Gb of compressed data in this directory. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/fr3/multiz8way 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 - alignments/ 2012-02-23 15:02 - fr3.8way.nh 2012-02-23 13:25 201 fr3.commonNames.8way.nh 2012-02-23 13:25 222 maf/ 2021-08-03 18:46 - md5sum.txt 2012-02-23 13:38 201 multiz8way.maf.gz 2012-02-21 13:55 705M