This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/multiz11way/README.txt This directory contains compressed multiple alignments of the following assemblies to the Gorilla genome (gorGor3, May 2011): Assemblies used in these alignments: Gorilla gorilla gorilla May 2011 Sanger gorGor3.1/gorGor3 Chimp Pan troglodytes Oct. 2010 CGSC 2.1.3/panTro3 Human Homo sapiens Feb. 2009 GRCh37/hg19 Gibbon Nomascus leucogenys Jan. 2010 GGSC Nleu1.0/nomLeu1 Orangutan Pongo pygmaeus abelii Jul. 2007 WUGSC 2.0.2/ponAbe2 Baboon Papio hamadryas Nov. 2008 Baylor 1.0/papHam1 Rhesus Macaca mulatta Jan. 2006 MGSC Merged 1.0/rheMac2 Marmoset Callithrix jacchus Mar. 2009 WUGSC 3.2/calJac3 Tarsier Tarsius syrichta Aug. 2008 Broad/tarSyr1 Mouse lemur Microcebus murinus Jun. 2003 Broad/micMur1 Bushbaby Otolemur garnettii Dec. 2006 Broad/otoGar1 These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=gorGor3&g=cons11way based on the phylogenetic tree: gorGor3.11way.nh. Files in this directory: - gorGor3.11way.nh - phylogenetic tree used during the multiz multiple alignment - gorGor3.commonNames.11way.nh - same as 11way.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 (gorGor3, May 2010) aligned to the assemblies. The multiz11way.maf.gz file contains all the alignments for all contigs in the X. tropicalis 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 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/gorGor3/phastCons11way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/phyloP11way --------------------------------------------------------------- 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 3.9 Gb of compressed data in this directory. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/multiz11way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/gorGor3/multiz11way 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/ 2011-12-09 09:53 - gorGor3.11way.nh 2011-12-08 11:18 312 gorGor3.commonNames.11way.nh 2011-12-08 11:19 290 maf/ 2019-11-06 10:58 - md5sum.txt 2011-12-08 13:37 212 multiz11way.maf.gz 2011-12-06 09:47 3.9G