This directory contains the Drosophila pseudoobscura Flybase 
Release 1.0 assembly (Nov. 2004).  
The annotations are from UCSC and collaborators worldwide.

If you plan 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 to 
hgdownload.cse.ucsc.edu, then go to the directory 
goldenPath/dp3/bigZips. To download multiple files, use 
the "mget" command:

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

dp3.2bit - contains the complete D. pseudoobscura/dp3 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

chromFa.zip - The assembly sequence chromosome 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.  RepeatMasker March 2004 version with
    RepBase libraries: RepBase Update 8.4, RM database version
    20040225.

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 done
    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 chromosomes.  

est.fa.gz - D. pseudoobscura 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. pseudoobscura mRNA from GenBank. 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.

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      dp3.2bit                2004-11-15 23:36   35M  
      dp3.chrom.sizes         2004-11-16 10:36  336   
      chromOut.zip            2004-11-16 14:04  2.8M  
      chromFa.zip             2004-11-16 14:06   41M  
      chromTrf.zip            2004-11-16 14:06  926K  
      chromFaMasked.zip       2004-11-16 14:16   39M  
      md5sum.txt              2014-02-03 11:49  235   
      xenoMrna.fa.gz          2016-03-18 16:52  5.0G  
      xenoMrna.fa.gz.md5      2016-03-18 16:53   49   
      mrna.fa.gz              2019-10-15 16:58  100K  
      mrna.fa.gz.md5          2019-10-15 16:58   45   
      est.fa.gz               2019-10-15 17:02   13M  
      est.fa.gz.md5           2019-10-15 17:02   44   
      xenoRefMrna.fa.gz       2019-10-15 17:02  331M  
      xenoRefMrna.fa.gz.md5   2019-10-15 17:02   52   
      dp3.fa.gz               2020-01-23 02:21   41M