This directory contains the Drosophila pseudoobscura Freeze 1 assembly 
(dp2, Aug. 2003) from the Baylor College of Medicine HGSC Drosophila 
Genome Project.  

Files included in this directory:

dp2.2bit - contains the complete D. pseudoobscura/dp2 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

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.

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.


dp2.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/dp2/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                             -   
      dp2.2bit                2004-08-03 09:03   33M  
      dp2.chrom.sizes         2004-08-09 15:46   21K  
      dp2.fa.gz               2020-01-23 02:21   40M  
      est.fa.gz               2019-10-17 02:01   13M  
      est.fa.gz.md5           2019-10-17 02:01   44   
      md5sum.txt              2014-05-05 16:00  247   
      mrna.fa.gz              2019-10-17 01:57  100K  
      mrna.fa.gz.md5          2019-10-17 01:57   45   
      scaffoldFa.zip          2004-08-16 19:50   40M  
      scaffoldFaMasked.zip    2004-08-16 19:51   38M  
      scaffoldOut.zip         2004-08-16 19:46  2.7M  
      scaffoldTrf.zip         2004-08-16 19:50  919K  
      xenoMrna.fa.gz          2016-03-14 16:37  5.0G  
      xenoMrna.fa.gz.md5      2016-03-14 16:38   49   
      xenoRefMrna.fa.gz       2019-10-17 02:01  331M  
      xenoRefMrna.fa.gz.md5   2019-10-17 02:01   52