This directory contains compressed FASTA alignments for the CDS regions
of the Fugu genome (FUGU5/fr3, Oct. 2011) aligned to the following assemblies:
Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3
Tetraodon Tetraodon nigroviridis Mar. 2007 Genoscope 8.0/tetNig2
Nile tilapia Oreochromis niloticus Jan. 2011 Broad/oreNil1
Stickleback Gasterosteus aculeatus Feb. 2006 Broad/gasAcu1
Atlantic cod Gadus morhua May. 2010 Genofisk/gadMor1
Medaka Oryzias latipes Oct. 2005 NIG/oryLat2
Zebrafish Danio rerio Jul. 2010 Zv9/danRer7
Coelacanth Latimeria chalumnae Aug. 2011 Broad/latCha1
Files included in this directory:
- ensGene.exonAA.fa.gz: for each exon in the Fugu/fr3 Ensembl Gene
track, this file contains either amino acids (AA) or nucleotides (Nuc) for
fr3 and the aligning genomes.
- ensGene.exonNuc.fa.gz: for each exon in the Fugu/fr3 Ensembl
set of genes, this file contains either amino acids (AA) or
nucleotides (Nuc) for Fugu/fr3 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/fr3/multiz8way/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 -
ensGene.exonAA.fa.gz 2012-02-23 14:49 106M
ensGene.exonNuc.fa.gz 2012-02-23 14:52 186M
md5sum.txt 2012-02-23 14:58 133