This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz4way/README.txt This directory contains compressed multiple alignments of the following assemblies to the human genome (hg38, Dec. 2013): Assemblies used in these alignments: Human Homo sapiens Dec. 2013 (GRCh38/hg38) reference Mouse Mus musculus Dec. 2011 (GRCm38/mm10) Chinese tree shrew Tupaia chinensis Jan. 2013 (BGI TupChi_1.0/tupChi1) Malayan flying lemur Galeopterus variegatus Jun. 2014 (WashU G_variegatus-3.0.2/galVar1) These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons4way based on the phylogenetic tree: hg38.4way.nh. Files in this directory: - hg38.4way.nh - phylogenetic tree used during the multiz multiple alignment - hg38.4way.commonNames.nh - same as hg38.4way.nh with the UCSC database names replaced by the common name for the species - hg38.4way.scientificName.nh - same as hg38.4way.nh with the UCSC database names replaced by the scientific name for the species - upstream*.knownGene.maf.gz - alignments of regions upstream of UCSC genes - hg38.4way.maf.gz - the multiple alignments on the human genome - md5sum.txt - md5 check sums of these files to verify correct download files The "alignments" directory contains compressed FASTA alignments for the CDS regions for the gene track knownGene (March 2016 version) of the human genome (hg38, Dec. 2013) aligned to the assemblies. The hg38.4way.maf.gz file contain all the alignments for the chromosomes in the human 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 3.0 Gb, uncompressed is more than 13 Gb. The .upstream*.*.maf.gz files contain alignments in regions upstream of annotated transcription starts for version 81/July 2015 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. 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/hg38/phastCons4way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP4way --------------------------------------------------------------- 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 240 Mb of compressed data in this directory. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz4way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/hg38/multiz4way 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/ 2017-04-21 13:22 - hg38.4way.commonNames.nh 2017-04-21 14:23 116 hg38.4way.maf.gz 2017-04-20 16:20 2.5G hg38.4way.nh 2017-04-21 14:23 90 hg38.4way.scientificNames.nh 2017-04-21 14:23 130 md5sum.txt 2017-04-21 16:31 457 upstream1000.knownGene.maf.gz 2017-04-21 14:53 32M upstream2000.knownGene.maf.gz 2017-04-21 14:59 56M upstream5000.knownGene.maf.gz 2017-04-21 15:04 121M