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.