This directory contains the Drosophila virilis 12 July 2004 assembly 
from Agencourt Bioscience Corporation.  

Files included in this directory:

md5sum.txt - MD5 checksum of these files to verify correct transmission.

droVir1.2bit - contains the complete D. virilis/droVir1 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

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

scaffoldFa.zip - The working draft sequence in one file per scaffold.
    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 scaffold.

scaffoldFaMasked.zip - The working draft sequence in one file per
    scaffold. Repeats are masked by capital N's and non-repeating
    sequence is shown in upper case.

scaffoldOut.zip - RepeatMasker .out file for scaffolds.  These were 
    created with RepeatMasker at the -s sensitive setting.

scaffoldTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file 
    per scaffold.  

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.


droVir1.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 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/droVir1/bigZips. To download multiple files, use the "mget" 
command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
 
These data have been freely provided by Agencourt Bioscience Corporation
before publication for use in the UCSC Genome Browser 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, provided that the Agencourt is properly acknowledged. 

3. Agencourt reserves the right to publish the initial large-scale analyses 
   of the dataset, including large-scale identification of regions of 
   evolutionary conservation and large-scale genomic assembly. 

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


[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 3.1K 
[TXT]README.txt.bak28-Jan-2014 16:19 3.0K 
[   ]droVir1.2bit07-Nov-2004 15:47 50M 
[   ]droVir1.chrom.sizes05-Nov-2004 11:49 525K 
[TXT]md5sum.txt03-Feb-2014 11:48 251  

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