This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/README.txt This directory contains compressed multiple alignments of the following assemblies to the X. tropicalis genome (xenTro3, Nov 2009): Assemblies used in these alignments: - X. tropicalis Xenopus tropicalis Nov. 2009 xenTro3/JGI 4.2 - Lizard Anolis carolinensis May 2010 anoCar2/Broad - Chicken Gallus gallus May 2006 galGal3/WUGSC 2.1 - Turkey Meleagris gallopavo Dec. 2009 melGal1/TGC Turkey_2.01 - Opossum Monodelphis domestica Oct. 2006 monDom5/Broad - Rat Rattus norvegicus Nov. 2004 rn4/Baylor 3.4 - Mouse Mus musculus Jul. 2007 mm9/NCBI37 - Human Homo sapiens Feb. 2009 hg19/GRCh37 - Zebrafish Danio rerio Jul. 2010 danRer7/Zv9 These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro3&g=cons9way based on the phylogenetic tree: 9way.nh. Files in this directory: - 9way.nh - phylogenetic tree used during the multiz multiple alignment - xenTro3.commonNames.9way.nh - same as 9way.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 (xenTro3, May 2010) aligned to the assemblies. The multiz9way.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 3 Gb. (664 Mb 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/xenTro3/phastCons9way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phyloP9way --------------------------------------------------------------- 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 31 Gb of compressed data in this directory. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/xenTro3/multiz9way 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 - 9way.nh 2011-09-29 15:27 225 alignments/ 2011-09-30 17:20 - maf/ 2019-11-06 11:19 - md5sum.txt 2011-10-04 11:23 387 multiz9way.maf.gz 2011-09-28 14:14 663M upstream1000.ensGene.maf.gz 2011-10-04 11:05 13M upstream2000.ensGene.maf.gz 2011-10-04 11:11 22M upstream5000.ensGene.maf.gz 2011-10-04 11:17 59M xenTro3.commonNames.9way.nh 2011-09-29 15:28 230