This directory contains the Mar. 2006 chromosome-based chimpanzee
assembly produced by Washington University, St. Louis.  It is
based on the Oct. 2005 6X draft assembly (Build 2 Version 1), 
produced by the Chimpanzee Genome Sequencing Consortium.

The whole genome shotgun sequence data were assembled using PCAP 
by the Washington University Genome Sequencing
Center. The underlying whole genome shotgun data were generated at the
Washington University School of Medicine and the Broad Institute.

A 5-megabase region of chromosome 7 was finished at the Washington
University Genome Sequencing Center (chr7:84674857-89461887). The
chromosome Y sequence was finished at the Washington University Genome
Sequencing Center with detailed mapping and extensive collaboration
with the Broad Institute.

This assembly also contains finished chromosome 21 sequence from the Riken
Genome Sciences Center.

Files included in this directory:

  - chr*.fa.zip: compressed FASTA sequence of each chromosome.
    Each chromosome is in a separate file in a zipped Fasta format. 

    Repeats -- which are shown in lower case -- are annotated by 
    RepeatMasker run at the sensitive setting.  The RepeatMasker 
    version used was: 
        1.11 2006/01/20 (open 3-1-3)
    The RepeatMasker pan_troglodytes library was used, with the
    addition of 2 subtelomeric satellite repeats provided by
    the Evan Eichler lab.  The library version used was:
        20060119
    Tandem repeats of period 12 or less are also masked out 
    using Tandem Repeats Finder.

The main assembly is contained in the chrN.fa files, where N is the 
name of the chromosome.  The chrN_random.fa files contain sequence that 
cannot be placed with certainty at a specific place on the chromosome. 

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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/panTro2/chromosomes. To download multiple 
files, use the "mget" command:

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

The chimp sequence is made freely available before scientific 
publication 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 
   particular genes and regions 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.