This directory contains compressed FASTA alignments for the CDS regions
of the Gorilla genome (Sanger gorGor3.1/gorGor3, May 2011) aligned to the 
following assemblies:

Gorilla gorilla gorilla                 May  2011   Sanger gorGor3.1/gorGor3
Chimp           Pan troglodytes         Oct. 2010   CGSC 2.1.3/panTro3
Human           Homo sapiens            Feb. 2009   GRCh37/hg19
Gibbon          Nomascus leucogenys     Jan. 2010   GGSC Nleu1.0/nomLeu1
Orangutan       Pongo pygmaeus abelii   Jul. 2007   WUGSC 2.0.2/ponAbe2
Baboon          Papio hamadryas         Nov. 2008   Baylor 1.0/papHam1
Rhesus          Macaca mulatta          Jan. 2006   MGSC Merged 1.0/rheMac2
Marmoset        Callithrix jacchus      Mar. 2009   WUGSC 3.2/calJac3
Tarsier         Tarsius syrichta        Aug. 2008   Broad/tarSyr1
Mouse lemur     Microcebus murinus      Jun. 2003   Broad/micMur1
Bushbaby        Otolemur garnettii      Dec. 2006   Broad/otoGar1

Files included in this directory:
  - ensGene.exonAA.fa.gz: for each exon in the Gorilla/gorGor3 Ensembl Gene
    track, this file contains either amino acids (AA) or nucleotides (Nuc) for
    gorGor3 and the aligning genomes.
  - ensGene.exonNuc.fa.gz: for each exon in the Gorilla/gorGor3 Ensembl
    set of genes, this file contains either amino acids (AA) or
    nucleotides (Nuc) for Gorilla/gorGor3 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/gorGor3/multiz11way/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.