This directory contains the Release 3.1 (Jan. 2003, UCSC version dm1) 
assembly of the Drosophila melanogaster genome (dm1). 

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.

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.

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.


dm1.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/dm1/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.


      Name                    Last modified      Size  Description
Parent Directory - dm1.chrom.sizes 2003-10-05 13:29 154 chromOut.zip 2003-10-29 13:45 2.1M chromFa.zip 2003-10-29 13:47 39M chromFaMasked.zip 2003-10-29 13:51 34M chromTrf.zip 2003-10-29 13:51 286K dm1.2bit 2014-04-30 10:28 31M dm1.2bit.md5 2014-05-07 15:24 43 xenoMrna.fa.gz 2016-03-14 15:09 4.9G xenoMrna.fa.gz.md5 2016-03-14 15:09 49 dm1.fa.gz 2020-01-23 02:21 39M mrna.fa.gz 2020-02-28 00:08 40M mrna.fa.gz.md5 2020-02-28 00:08 45 est.fa.gz 2020-02-28 00:13 109M est.fa.gz.md5 2020-02-28 00:13 44 xenoRefMrna.fa.gz 2020-02-28 00:13 308M xenoRefMrna.fa.gz.md5 2020-02-28 00:13 52 refMrna.fa.gz 2020-02-28 00:13 29M refMrna.fa.gz.md5 2020-02-28 00:13 48