This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz5way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the human genome (hg38/GRCh38, Dec. 2013):
Assemblies used in these alignments: (alignment
type)
Human - Homo sapiens - Dec. 2013 (GRCh38/hg38) reference
Malayan flying lemur -
Galeopterus variegatus Jun. 2014 (WashU 3.0.2/galVar1) syntenic
Chinese tree shrew - Tupia chinensis Jan. 2013 (BGI CR_1.0/tupChi1) syntenic
Guinea pig - Cavia porcellus Feb. 2008 (Broad/cavPor3) syntenic
Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic
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These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons5way
based on the phylogenetic tree: hg38.5way.nh
Files in this directory:
- hg38.5way.nh - phylogenetic tree used during the multiz multiple alignment
- hg38.5way.commonNames.nh - same as hg38.5way.nh with the UCSC database
name replaced by the common name for the species
- upstream1000.knownGene.maf.gz - alignments in regions upstream, see below
- upstream2000.knownGene.maf.gz - alignments in regions upstream, see below
- upstream5000.knownGene.maf.gz - alignments in regions upstream, see below
- hg38.5way.maf.gz - alignmens with gap annotation
See also:
http://genomewiki.ucsc.edu/index.php/Hg38_5-way_conservation_alignment
The "alignments" directory contains compressed FASTA alignments
for the UCSC Known Gene CDS regions of the human genome
(hg38, Dec. 2013) aligned to the assemblies. Additional
alignment files are provided for RefSeq genes, and the
UCSC Known Gene canonical genes.
The hg38.5way.maf.gz file contains the alignments to
the human assembly, with additional annotations to
indicate gap context, and genomic breaks for the
sequence in the underlying genome assemblies. Beware, the compressed
data size of this file is 3.2 Gb, uncompressed is approximately 13 Gb.
The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for UCSC Known 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
mouse, 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 the human sequence; 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/phastCons5way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP5way
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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 -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz5way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg38/multiz5way
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.
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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 -
hg38.5way.maf.gz 2017-12-17 22:37 3.2G
upstream5000.knownGene.maf.gz 2017-12-18 12:18 157M
upstream2000.knownGene.maf.gz 2017-12-18 12:08 71M
upstream1000.knownGene.maf.gz 2017-12-18 11:59 41M
md5sum.txt 2017-12-18 12:44 412
hg38.5way.scientificNames.nh 2017-12-18 11:38 169
hg38.5way.commonNames.nh 2017-12-18 11:38 150
hg38.5way.nh 2017-12-18 11:37 128