This directory contains compressed FASTA alignments for the CDS regions
of the mouse genome (mm9, Mar. 2006) aligned to the
following assemblies:
_ mouse Mus musculus July 2007, mm9
_ rat Rattus norvegicus Nov 2004, rn4
_ guinea pig Cavia porcellus Oct 2005, cavPor2
_ rabbit Oryctolagus cuniculus May 2005, oryCun1
_ human Homo sapiens Mar 2006, hg18
_ chimpanzee Pan troglodytes Mar 2006, panTro2
_ orangutan Pongo pygmaeus abelii July 2007, ponAbe2
_ rhesus Macaca mulatta Jan 2006, rheMac2
_ marmoset Callithrix jacchus June 2007, calJac1
_ bushbaby Otolemur garnetti Dec 2006, otoGar1
_ tree shrew Tupaia belangeri Dec 2006, tupBel1
_ shrew Sorex araneus June 2006, sorAra1
_ hedgehog Erinaceus europaeus June 2006, eriEur1
_ dog Canis familiaris May 2005, canFam2
_ cat Felis catus Mar 2006, felCat3
_ horse Equus caballus Jan 2007, equCab1
_ cow Bos taurus Aug 2006, bosTau3
_ armadillo Dasypus novemcinctus May 2005, dasNov1
_ elephant Loxodonta africana May 2005, loxAfr1
_ tenrec Echinops telfairi July 2005, echTel1
_ opossum Monodelphis domestica Jan 2006, monDom4
_ platypus Ornithorhychus anatinus Mar 2007, ornAna1
_ chicken Gallus gallus May 2006, galGal3
_ lizard Anolis carolinensis Feb 2007, anoCar1
_ frog 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 Apr 2006, oryLat1
_ zebrafish Danio rerio July 2007, danRer5
Files included in this directory:
- knownGene.exon*.fa.gz: for each exon in the mm9 UCSC Gene track, this
file contains either amino acids (AA) or nucleotides (Nuc) for mm9 and
the aligning genomes.
- knownCanonical.exon*.fa.gz: for each exon in the mm9 canonical set of
UCSC Genes, this file contains either amino acids (AA) or
nucleotides (Nuc) for mm9 and the aligning genomes.
- refGene.exon*.fa.gz: for each exon in the mm9 RefSeq Gene track, this
file contains either amino acids (AA) or nucleotides (Nuc) for mm9
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/mm9/multiz30way/alignment
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 -
md5sum.txt 2008-10-02 15:04 351
knownCanonical.exonAA.fa.gz 2008-10-01 19:43 131M
refGene.exonAA.fa.gz 2008-09-30 20:15 142M
knownCanonical.exonNuc.fa.gz 2008-10-01 19:45 221M
knownGene.exonAA.fa.gz 2008-10-01 15:15 221M
refGene.exonNuc.fa.gz 2008-09-30 20:17 243M
knownGene.exonNuc.fa.gz 2008-10-01 15:20 402M