This directory contains the Jul. 2007 assembly of the orangutan genome
(ponAbe2, WUSTL Pongo_albelii-2.0.2) in one gzip-compressed FASTA file 
per chromosome.

This assembly was produced by the Genome Sequencing Center at the Washington 
University School of Medicine in St. Louis.
For more information on the orangutan genome, see the project website:
http://genome.wustl.edu/genome.cgi?GENOME=Pongo%20abelii

Files included in this directory:

  - chr*.fa.gz: compressed FASTA sequence of each chromosome.

    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.

    RepeatMasker was run with the -s (sensitive) setting.
    RepeatMasker version May 17 2007 (open-3-1-8)
    library version RELEASE 20061006

------------------------------------------------------------------
If you plan 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 to hgdownload.cse.ucsc.edu, then 
go to the directory goldenPath/ponAbe2/chromosomes. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

------------------------------------------------------------------
Alternate methods to ftp access.
    
Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/ .
For a single file, e.g. chrM.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/chrM.fa.gz .
    
Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/chromosomes/chrM.fa.gz' 
        -O chrM.fa.gz
    
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

------------------------------------------------------------------
The Orangutan sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases.

2. Users are free to use the data in scientific papers analyzing these data
   if the providers of these data are properly acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. The centers producing the data reserve the right to publish the initial
   large-scale analyses of the data set, including large-scale identification
   of regions of evolutionary conservation and large-scale genomic assembly.
   Large-scale refers to regions with size on the order of a chromosome (that
   is, 30 Mb or more).

4. Any redistribution of the data should carry this notice.