This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/multiz12way/README.txt
This directory contains compressed multiple alignments of
12 genomes to the Danio rerio/danRer10/Sept. 2014 zebrafish genome.
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer10&g=cons12way
based on the phylogenetic tree: danRer10.12way.nh.
danRer10.12way.maf.gz
Files in this directory:
- danRer10.12way.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.
- danRer10.12way.scientificName.nh - same as danRer10.12way.nh with the
sequence name replaced with the scientific name for the species.
- danRer10.12way.commonNames.nh - same as danRer10.12way.nh with the sequence
name replaced with the common name
- danRer10.12way.maf.gz - multiple alignments on zebrafish
- upstream*.ensGene.maf.gz - alignments of regions upstream of
Ensembl genes
- 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: ensGene,
of the zebrafish genome (danRer10, Sept. 2014) aligned to the assemblies.
The danRer10.12way.maf.gz file contains all the alignments on the zebrafish
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 1.2 Gb, uncompressed is approximately 5.4 Gb.
The upstream*.ensGene.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
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/danRer10/phastCons12way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/phyloP12way
---------------------------------------------------------------
Assemblies used in these alignments:
Zebrafish Danio rerio Sep. 2014 (GRCz10/danRer10) (reference)
Stickleback Gasterosteus aculeatus Feb. 2006 (Broad/gasAcu1) (maf net)
Medaka Oryzias latipes Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (maf net)
Tetraodon Tetraodon nigroviridis Mar. 2007
(Genoscope 8.0/tetNig2) (maf net)
Fugu Takifugu rubripes Oct. 2011 (FUGU5/fr3) (maf net)
Spotted gar Lepisosteus oculatus Dec 2011 (LepOcu1/lepOcu1) (maf net)
Human Homo sapiens Dec. 2013 (GRCh38/hg38) (maf net)
Mouse Mus musculus Dec. 2011 (GRCm38/mm10) (maf net)
Chicken Gallus gallus Mar. 2018 (GRCg6a/galGal6) (maf net)
X. tropicalis Xenopus tropicalis Jul. 2016
(Xenopus_tropicalis_v9.1/xenTro9) (maf net)
Coelacanth Latimeria chalumnae Aug. 2011 (Broad/latCha1) (maf net)
Elephant shark Callorhinchus milii Dec. 2013
(Callorhinchus_milii-6.1.3/calMil1) (maf net)
---------------------------------------------------------------
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 40 Gb of compressed data in this directory,
approximately 340 Gb uncompressed.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer10/multiz12way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/danRer10/multiz12way
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/ 2025-04-09 09:19 -
danRer10.12way.commonNames.nh 2020-02-26 12:44 343
danRer10.12way.maf.gz 2020-03-09 12:13 1.1G
danRer10.12way.nh 2020-03-18 15:14 347
danRer10.12way.scientificNames.nh 2020-02-26 12:51 440
md5sum.txt 2020-03-18 16:03 471
upstream1000.ensGene.maf.gz 2020-03-18 16:01 19M
upstream2000.ensGene.maf.gz 2020-03-18 16:01 34M
upstream5000.ensGene.maf.gz 2020-03-18 16:01 117M