This directory contains the Release 4 (Apr. 2004, UCSC version dm2) 
assembly of the Drosophila melanogaster genome. 

Files included in this directory:

dm1.2bit - contains the complete D. melanogaster/dm1 genome sequence
    in the 2bit file format.  While we are providing the .2bit for
    this assembly, we will continue to use the .nib files in
    the Genome Browser.  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

chromFa.zip - The assembly 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.

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

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

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

est.fa.gz - D. melanogaster ESTs in GenBank. This sequence data is updated 
    once a week via automatic GenBank updates.

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

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

refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
    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.zip - Same as upstream1000, but 2000 bases.

upstream5000.zip - 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.


dm2.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/dm2/bigZips. To download multiple files, use 
the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
 
All the files in this directory are freely available for public use.


[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 3.3K 
[TXT]README.txt.bak06-May-2014 16:04 3.2K 
[   ]dm2.2bit03-Jul-2005 09:10 32M 
[   ]dm2.chrom.sizes09-Sep-2004 15:37 177  
[TXT]md5sum.txt05-May-2014 15:31 280  
[   ]upstream1000.fa.gz11-Oct-2006 15:52 3.8M 
[   ]upstream2000.fa.gz11-Oct-2006 15:52 7.2M 
[   ]upstream5000.fa.gz11-Oct-2006 15:52 16M 

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