This directory contains compressed FASTA alignments for the CDS regions
of the human genome (hg19/GRCh37, Feb. 2009) aligned to the
following assemblies:
- Human Homo sapiens Feb. 2009 hg19/GRCh37
- Chimp Pan troglodytes Mar. 2006 panTro2
- Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
- Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
- Rhesus Macaca mulatta Jan. 2006 rheMac2
- Baboon Papio hamadryas Nov. 2008 papHam1
- Marmoset Callithrix jacchus June 2007 calJac1
- Tarsier Tarsius syrichta Aug. 2008 tarSyr1
- Mouse lemur Microcebus murinus Jun. 2003 micMur1
- Bushbaby Otolemur garnettii Dec. 2006 otoGar1
- Tree shrew Tupaia belangeri Dec. 2006 tupBel1
- Mouse Mus musculus July 2007 mm9
- Rat Rattus norvegicus Nov. 2004 rn4
- Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
- Guinea Pig Cavia porcellus Feb. 2008 cavPor3
- Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
- Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
- Pika Ochotona princeps Jul. 2008 ochPri2
- Alpaca Vicugna pacos Jul. 2008 vicPac1
- Dolphin Tursiops truncatus Feb. 2008 turTru1
- Cow Bos taurus Oct. 2007 bosTau4
- Horse Equus caballus Sep. 2007 equCab2
- Cat Felis catus Mar. 2006 felCat3
- Dog Canis lupus familiaris May 2005 canFam2
- Microbat Myotis lucifugus Mar. 2006 myoLuc1
- Megabat Pteropus vampyrus Jul. 2008 pteVam1
- Hedgehog Erinaceus europaeus June 2006 eriEur1
- Shrew Sorex araneus June 2006 sorAra1
- Elephant Loxodonta africana Jul. 2009 loxAfr3
- Rock hyrax Procavia capensis Jul. 2008 proCap1
- Tenrec Echinops telfairi July 2005 echTel1
- Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
- Sloth Choloepus hoffmanni Jul. 2008 choHof1
- Wallaby Macropus eugenii Nov. 2007 macEug1
- Opossum Monodelphis domestica Oct. 2006 monDom5
- Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
- Chicken Gallus gallus May 2006 galGal3
- Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
- Lizard Anolis carolinensis Feb. 2007 anoCar1
- X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
- Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
- Fugu Takifugu rubripes Oct. 2004 fr2
- Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
- Medaka Oryzias latipes Oct. 2005 oryLat2
- Zebrafish Danio rerio Dec. 2008 danRer6
- Lamprey Petromyzon marinus Mar. 2007 petMar1
Files included in this directory:
- knownGene.exon*.fa.gz: for each exon in the hg19/GRCh37 UCSC Gene track,
this file contains either amino acids (AA) or nucleotides (Nuc) for
hg19/GRCh37 and the aligning genomes.
- knownCanonical.exon*.fa.gz: for each exon in the hg19/GRCh37 canonical
set of UCSC Genes, this file contains either amino acids (AA) or
nucleotides (Nuc) for hg19/GRCh37 and the aligning genomes.
- refGene.exon*.fa.gz: for each exon in the hg19/GRCh37 RefSeq Gene track,
this file contains either amino acids (AA) or nucleotides (Nuc) for
hg19/GRCh37 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/hg19/multiz46way/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 -
knownCanonical.exonAA.fa.gz 2013-06-25 15:15 205M
knownCanonical.exonNuc.fa.gz 2013-06-25 15:18 336M
knownGene.exonAA.fa.gz 2013-06-25 11:46 542M
knownGene.exonNuc.fa.gz 2013-06-25 11:55 932M
md5sum.txt 2014-04-21 17:10 351
refGene.exonAA.fa.gz 2013-08-15 15:19 355M
refGene.exonNuc.fa.gz 2013-08-15 15:25 593M