This directory contains compressed FASTA alignments for the CDS regions
of the human genome (hg18, Mar. 2006) aligned to the
following assemblies:
_ Human Homo sapiens Mar. 2006 hg18
_ 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
_ 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
_ TreeShrew Tupaia belangeri Dec. 2006 tupBel1
_ Mouse Mus musculus July 2007 mm9
_ Rat Rattus norvegicus Nov. 2004 rn4
_ Kangaroo rat Dipodomys ordii July 2008 dipOrd1
_ Guinea Pig Cavia porcellus Feb. 2008 cavPor3
_ Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
_ Rabbit Oryctolagus cuniculus May 2005 oryCun1
_ Pika Ochotona princeps July 2008 ochPri2
_ Alpaca Vicugna pacos July 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 July 2008 pteVam1
_ Hedgehog Erinaceus europaeus June 2006 eriEur1
_ Shrew Sorex araneus June 2006 sorAra1
_ Elephant Loxodonta africana July 2008 loxAfr2
_ Rock hyrax Procavia capensis July 2008 proCap1
_ Tenrec Echinops telfairi July 2005 echTel1
_ Armadillo Dasypus novemcinctus July 2008 dasNov2
_ Sloth Choloepus hoffmanni July 2008 choHof1
_ Opossum Monodelphis domestica Jan. 2006 monDom4
_ Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
_ Chicken Gallus gallus May 2006 galGal3
_ Zebra finch Taeniopygia guttata July 2008 taeGut1
_ Lizard Anolis carolinensis Feb. 2007 anoCar1
_ X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
_ Tetraodon Tetraodon nigroviridis Feb. 2004 tetNig1
_ Fugu Takifugu rubripes Oct. 2004 fr2
_ Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
_ Medaka Oryzias latipes Oct. 2005 oryLat2
_ Zebrafish Danio rerio July 2007 danRer5
_ Lamprey Petromyzon marinus Mar. 2007 petMar1
Files included in this directory:
- knownGene.exon*.fa.gz: for each exon in the hg18 UCSC Gene track, this
file contains either amino acids (AA) or nucleotides (Nuc) for hg18 and the
aligning genomes.
- knownCanonical.exon*.fa.gz: for each exon in the hg18 canonical set of UCSC
Genes, this file contains either amino acids (AA) or nucleotides (Nuc)
for hg18 and the aligning genomes.
- refGene.exon*.fa.gz: for each exon in the hg18 RefSeq Gene track, this file
contains either amino acids (AA) or nucleotides (Nuc) for hg18 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/hg18/multiz44way/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 2008-12-07 18:09 435M
refGene.exonAA.fa.gz 2008-12-07 18:09 258M
md5sum.txt 2009-01-13 09:41 351
knownGene.exonNuc.fa.gz 2008-12-07 18:08 749M
knownGene.exonAA.fa.gz 2008-12-07 18:08 432M
knownCanonical.exonNuc.fa.gz 2008-12-07 18:08 310M
knownCanonical.exonAA.fa.gz 2008-12-07 18:08 189M