This directory contains compressed FASTA alignments for the CDS regions
of the rat genome (rn4, Nov. 2004) aligned to the following assemblies:
- mouse (Feb 2006, mm8)
- human (Mar 2006, hg18)
- dog (May 2005, canFam2)
- cow (Mar 2005, bosTau2)
- opossum (Jan 2006, monDom4)
- chicken (Feb 2004, galGal2)
- frog (Oct 2004, xenTro1)
- zebrafish (May 2005, danRer3)
Files included in this directory:
- refGene.exon*.fa.gz: for each exon in the Baylor 3.4/rn4 RefSeq Gene track,
this file contains either amino acids (AA) or nucleotides (Nuc) for
Baylor 3.4/rn4 and the aligning genomes.
- rgdGene2Canonical.exon*.fa.gz: for each exon in the Baylor 3.4/rn4
canonical set of RGD Genes 2, this file contains either amino acids (AA)
or nucleotides (Nuc) for Baylor 3.4/rn4 and the aligning genomes.
- rgdGene2.exon*.fa.gz: for each exon in the Baylor 3.4/rn4 RGD Genes 2 track,
this file contains either amino acids (AA) or nucleotides (Nuc) for
Baylor 3.4/rn4 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 -
refGene.exonAA.fa.gz 2011-10-10 16:24 37M
rgdGene2.exonAA.fa.gz 2011-09-30 13:32 40M
rgdGene2Canonical.exonAA.fa.gz 2011-10-10 16:02 41M
refGene.exonNuc.fa.gz 2011-10-10 16:25 63M
rgdGene2Canonical.exonNuc.fa.gz 2011-10-10 16:03 66M
rgdGene2.exonNuc.fa.gz 2011-09-30 13:33 66M