This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/multiz11way/README.txt This directory contains compressed multiple alignments of the following assemblies to the X. tropicalis genome (xenTro9, Jul. 2016): Assemblies used in these alignments: - X. tropicalis Xenopus tropicalis Jul. 2016 DOE JGI v9.1/xenTro9 reference genome - African clawed frog Xenopus laevis Aug. 2016 IXSC v2/xenLae2 - Tibetan frog Nanorana parkeri Mar. 2015 BGI ZX_2015/nanPar1 - Painted turtle Chrysemys picta bellii Mar. 2014 IPTGSC v3.0.3/chrPic2 - Chicken Gallus gallus May 2006 Gallus_gallus-5.0/galGal5 - Lizard Anolis carolinensis May 2010 anoCar2/Broad - Opossum Monodelphis domestica Oct. 2006 Broad/monDom5 - Dog Canis lupus familiaris Sep. 2011 Broad CanFam3.1/canFam3 - Human Homo sapiens Dec. 2013 GRCh38/hg38 - Mouse Mus musculus Dec. 2011 GRCm38/mm10 - Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3 Syntenic net filtered MAF files used for multiz: hg38, mm10, xenLae2, canFam3, monDom5, fr3, galGal5, anoCar2 Reciprocal best filtered MAF files used for multiz: nanPar1 chrPic2 These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro9&g=cons11way based on the phylogenetic tree: xenTro9.11way.nh. Files in this directory: - xenTro9.11way.nh - phylogenetic tree used during the multiz multiple alignment - xenTro9.11way.commonNames.nh - same as xenTro9.11way.nh with the UCSC database names replaced by the common name for the species - xenTro9.11way.scientificName.nh - same as xenTro9.11way.nh with the UCSC database names replaced by the scientific name for the species - xenTro9.11way.maf.gz - the multiple alignments on the X. tropicalis reference genome - upstream*.refGene.maf.gz - alignments of regions upstream of refGene genes - md5sum.txt - md5 check sums of these files to verify correct download files The xenTro9.11way.maf.gz file contain all the alignments for the chromosomes in the X. tropicalis genome, including additional annotations to indicate gap context and genomic breaks for the sequence in the underlying genome assemblies. Note, the compressed data size of the maf file is 853 Mb, uncompressed is 4.0 Gb. The "alignments" directory contains compressed FASTA alignments for the CDS regions of the Xenopus genome (xenTro9, Jul. 2016) aligned to the assemblies. These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro9&g=cons11way based on the phylogenetic tree: xenTro9.11way.nh. 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/xenTro9/phastCons11way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/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 934 Mb of compressed data in this directory. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/multiz11way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/xenTro9/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/ 2017-05-02 16:48 - md5sum.txt 2017-05-02 14:50 422 upstream1000.refGene.maf.gz 2017-05-02 14:38 5.3M upstream2000.refGene.maf.gz 2017-05-02 14:39 8.8M upstream5000.refGene.maf.gz 2017-05-02 14:40 21M xenTro9.11way.commonNames.nh 2017-05-02 14:49 326 xenTro9.11way.maf.gz 2017-05-02 10:33 853M xenTro9.11way.nh 2017-05-02 14:48 301 xenTro9.11way.scientificNames.nh 2017-05-02 14:49 418