This directory contains compressed FASTA alignments for the CDS regions
of the human genome (hg38/GRCh38, Dec. 2013) aligned to the
following assemblies:
Assemblies used in these alignments: (alignment
type)
Human - Homo sapiens Dec. 2013 (GRCh38/hg38) reference
Baboon - Papio anubis Mar. 2012 (Baylor Panu_2.0/papAnu2) syntenic
Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) reciprocal best
Bonobo - Pan paniscus May. 2012 (Max-Planck/panPan1) reciprocal best
Chimp - Pan troglodytes Feb. 2011 (CSAC 2.1.4/panTro4) syntenic
Crab-eating macaque - Macaca fascicularis
Jun 2013 (Macaca_fascicularis_5.0/macFas5) syntenic
Gibbon - Nomascus leucogenys Oct. 2012 (GGSC Nleu3.0/nomLeu3) syntenic
Golden snub-nosed monkey - Rhinopithecus roxellana
Oct. 2014 (Rrox_v1/rhiRox1) reciprocal best
Gorilla - Gorilla gorilla gorilla May 2011 (gorGor3.1/gorGor3) reciprocal best
Green monkey - Chlorocebus sabaeus
Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) syntenic
Marmoset - Callithrix jacchus Mar. 2009 (WUGSC 3.2/calJac3) syntenic
Mouse lemur - Microcebus murinus Jul. 2007 (Broad/micMur1) reciprocal best
Orangutan - Pongo pygmaeus abelii Jul. 2007 (WUGSC 2.0.2/ponAbe2) syntenic
Proboscis monkey - Nasalis larvatus
Nov. 2014 (Charlie1.0/nasLar1) reciprocal best
Rhesus - Macaca mulatta Oct. 2010 (BGI CR_1.0/rheMac3) syntenic
Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) reciprocal best
Tarsier - Tarsius syrichta
Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reciprocal best
Tree shrew - Tupaia belangeri Dec. 2006 (Broad/tupBel1) reciprocal best
Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic
Dog - Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) syntenic
Files included in this directory:
- knownGene.exon*.fa.gz: for each exon in the hg38/GRCh38 Gencode Gene track,
this file contains either amino acids (AA) or nucleotides (Nuc) for
hg38/GRCh38 and the aligning genomes.
- knownCanonical.exon*.fa.gz: for each exon in the hg38/GRCh38 canonical
set of Gencode Genes, this file contains either amino acids (AA) or
nucleotides (Nuc) for hg38/GRCh38 and the aligning genomes.
- refGene.exon*.fa.gz: for each exon in the hg38/GRCh38 RefSeq Gene track,
this file contains either amino acids (AA) or nucleotides (Nuc) for
hg38/GRCh38 and the aligning genomes.
For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html
and http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA.
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To download a large file or multiple files from this directory, we recommend
that you use ftp rather than downloading the files via our website. To do so:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg38/multiz20way/alignments
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 -
refGene.exonNuc.fa.gz 2015-06-30 08:21 243M
refGene.exonAA.fa.gz 2015-06-30 08:19 157M
md5sum.txt 2015-06-30 18:33 423
knownGene.exonNuc.fa.gz 2015-06-29 20:18 369M
knownGene.exonAA.fa.gz 2015-06-29 20:15 233M
knownCanonical.exonNuc.fa.gz 2015-06-30 17:34 128M
knownCanonical.exonAA.fa.gz 2015-06-30 17:34 89M