This directory contains the Build 2 Version 1 (UCSC version 
panTro2) chimpanzee 6X draft assembly produced by the Chimp 
Genome Sequencing Consortium. 

Files included in this directory:

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

chromFa.tar.gz - The working draft sequence in one file per chromosome.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are in lower case while non-repeating sequence is
    in upper case.  The main assembly is in the chrN.fa files where N
    is the name of the chromosome.  The chrN_random.fa files contain
    clones which are either not yet finished, or which cannot be
    placed with certainty at a specific place on the chromosome.

chromFaMasked.tar.gz - The working draft sequence in one file per 
    chromosome. Repeats are masked by capital N's and
    non-repeating sequence is shown in upper case.  

chromOut.tar.gz - RepeatMasker .out file for chromosomes, created
    with RepeatMasker at the -s sensitive setting.

chromQuals.tar.gz - Quality scores for all bases in the assembly,
    in one file per chromosome.

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep 
    repeats with period of less than or equal to 12, and translated 
    into one .bed file per chromosome.  

est.fa.gz - Chimp and human ESTs in GenBank. This sequence data is
    updated once a week via automatic GenBank updates.

panTro2.2bit - contains the complete chimp/panTro2 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

panTro2.quals.fa.gz - quality scores in fasta file format

md5sum.txt - checksum file

mrna.fa.gz - Chimp and human 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 RefSeq genes with annotated 5' UTRs.  
    This file is updated weekly so it could be slightly out      
    of sync with the 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.


panTro2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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If you plan to download a large file or multiple files from this 
directory, we recommend 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/bigZips. To download multiple files, 
use the "mget" command:

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