This directory contains the Apr. 2006 assembly of the D. melanogaster genome
(dm3, BDGP Release 5), as well as repeat annotations and GenBank sequences.

This assembly was produced by the Berkeley Drosophila Genome Project.
For more information on the D. melanogaster genome, see the release notes:
  http://www.fruitfly.org/sequence/release5genomic.shtml

Files included in this directory:

dm3.2bit - contains the complete D. melanogaster/dm3 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.
    The May 17 2007 (open-3-1-8) version of RepeatMasker and library release
    20061006 were used.

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).

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

md5sum.txt - checksums of files in this directory

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 FlyBase genes with annotated 5' UTRs.

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.
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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 hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/dm3/bigZips

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

All the files in this directory are freely available for public use.