This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/regenRn1/multiz7way/README.txt This directory contains compressed multiple alignments of 6 genomes to the rat/regenRn1/May 2019 genome. These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=regenRn1&g=cons7way based on the phylogenetic tree: regenRn1.7way.nh. Files in this directory: - regenRn1.7way.nh - phylogenetic tree used during the multiz multiple alignment, using the UCSC database name, or sequence name for those sequences that are not hosted in UCSC databases. - regenRn1.7way.scientificName.nh - same as regenRn1.7way.nh with the sequence name replaced with the scientific name for the species. regenRn1.7way.commonNames.nh - same as regenRn1.7way.nh with the sequence name replaced with the common name - upstream*.ncbiRefSeq.maf.gz - alignments of regions upstream of NCBI RefSeq genes - maf/chr*.maf.gz - the multiple alignments on chicken for each chromosome - 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 three gene tracks, ws245Genes, refGene, ensGene, of the chicken genome (regenRn1, Mar. 2018) aligned to the assemblies. The maf/chr*.maf.gz files contain all the alignments for the chromosomes in the chicken 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 these maf files is 2.8 Gb, uncompressed is approximately 12 Gb. The upstream*.ncbiRefSeq.maf.gz files contain alignments in regions upstream of annotated transcription starts for NCBI RefSeq 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 chicken, 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 chicken; 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/regenRn1/phastCons7way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/regenRn1/phyloP7way --------------------------------------------------------------- Assemblies used in these alignments: Rat Rattus norvegicus May. 2019 (Regen Rn1/regenRn1) (reference) Mouse Mus musculus Dec. 2011 (GRCm38/mm10) (syntenic) Rabbit Oryctolagus cuniculus Apr. 2009 (Broad/oryCun2) (syntenic) Human Homo sapiens Dec. 2013 (GRCh38/hg38) (syntenic) Crab-eating macaque Macaca fascicularis Jun. 2013 (Macaca_fascicularis_5.0/macFas5) (syntenic) Pig Sus scrofa Feb. 2017 (Sscrofa11.1/susScr11) (syntenic) Dog Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) (syntenic) --------------------------------------------------------------- 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 3.1 Gb of compressed data in this directory, approximately 13.1 Gb uncompressed. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/regenRn1/multiz7way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/regenRn1/multiz7way To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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.