This directory contains the Drosophila pseudoobscura Freeze 1 assembly 
(Aug. 2003) from the Baylor College of Medicine HGSC Drosophila 
Genome Project.  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/dp1/bigZips. To download multiple files, use 
the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
 
Note: since the scaffolds have not yet been ordered and oriented 
on the chromosomes yet, we have lumped them all together into 
one "chromosome", chrUn, for our genome browser.  Downloads 
are available in chrUn coords as well as in scaffold coords.

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chromFa.zip - The working draft 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 working draft sequence in one file per
    chromosome. Repeats are masked by capital N's 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.  

liftAll.zip - A file that contains the offsets of scaffolds within
    chromosomes. 

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 scaffold.  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.

scaffoldAnnot.zip - Annotations in scaffold coordinates: 
    - BDGP D. melanogaster Genes, translated into D. pseudoobscura coords 
      using liftOver and the chained D. mel./D. pseudo. alignments.