This directory contains the Jul. 2007 assembly of the orangutan genome
(ponAbe2, WUSTL Pongo_albelii-2.0.2), as well as repeat annotations and 
GenBank sequences.

This assembly was produced by the Genome Sequencing Center at the Washington 
University School of Medicine in St. Louis, MO, USA.
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:

ponAbe2.2bit - contains the complete orangutan/ponAbe2 genome sequence
    in the 2bit file format.  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.  The utility program, twoBitToFa (available
    from the kent src tree), can be used to extract .fa file(s) from
    this file.  A pre-compiled version of the command line tool can be
    found at:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
	http://genome.ucsc.edu/admin/jk-install.html

chromAgp.tar.gz - Description of how the assembly was generated from
    fragments, unpacking to one file per chromosome.

chromFa.tar.gz - The assembly sequence in one file per 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.

chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
    RepeatMasker was run with the -s (sensitive) setting.
    RepeatMasker version May 17 2007 (open-3-1-8)
    library version RELEASE 20061006

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format (one file per chromosome).

ponAbe2.quality.fa.tar.gz - quality scores, individual fasta files for
	each chrom.
	Beware, this is 20Gb of data when unpacked and uncompressed

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Orangutan mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts for Xeno RefSeq genes with annotated 5' UTRs.  
    This file is updated weekly so it could be slightly out 
    of sync with the Xeno RefSeq data which is updated daily for most 
    assemblies.

upstream2000.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - Same as upstream1000, but 5000 bases.

xenoMrna.fa.gz - GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.

ponAbe2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

------------------------------------------------------------------
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/bigZips. 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/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.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.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 5.1K 
[   ]chromAgp.tar.gz01-Oct-2007 17:33 10M 
[   ]chromFa.tar.gz01-Oct-2007 17:49 960M 
[   ]chromFaMasked.tar.gz01-Oct-2007 17:57 506M 
[   ]chromOut.tar.gz01-Oct-2007 17:34 173M 
[   ]chromTrf.tar.gz01-Oct-2007 17:57 7.6M 
[TXT]md5sum.txt03-Jan-2014 15:09 361  
[   ]ponAbe2.2bit19-Sep-2007 14:31 858M 
[   ]ponAbe2.chrom.sizes12-Sep-2007 12:21 1.0K 
[   ]ponAbe2.quality.fa.tar.gz14-Oct-2008 10:24 726M 
[   ]ponAbe2.quals.fa.gz08-Jun-2009 13:24 746M 

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