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repetitive DNA

ckennedy at ems.salk.edu ckennedy at ems.salk.edu
Thu Jan 11 20:11:36 EST 2001


I am working on a tiny piece of the Drosophila genome project.
I am trying to assemble regions
from the base of the arms, 
where Celera assemblies stop, and progress towards the centromeres.

The tools i have been provided are Phred,Phrap, Consed, and blast.
My computers are Solaris 7 on sun hardware, Linux 2.2.18 on an iBook,
and Irix 6.5 on SGI Octane.

My project is BACs subcloned into 3kb and 10kb chunks.

One of the problems i have been struggling with is that the region
contains some repetitive DNA elements, some large repeats that
are highly identical, and some of the repeats are larger than my clone
I was thinking about attacking the problem with a divide and defeat
tactic, but i am new to thinking about how to assemble this gnarly
DNA.  What i was thinking of is this:

	1. make some fake projects
        2. copy the files from all the clones i know or strongly 
            suspect overlap into this fake project. 
	3. assemble fake without interference from highly identical 
            sequences some large distance away. 
	4. export the consensus as a high quality 'phd' file
            as a guide for phrap
	5. reassemble the BAC with these guides in place
I was thinking of using a similar tactic for 3 and 10 kb clones that 
are obviously placed incorrectly. 

some questions I have :

Am I approaching this entirely wrong ?

Does anyone have any suggestions or hints for working with repeats ?

Are there traditional ways to approach this problem ?

Are there any new assemblers that were designed to address
    repetitive DNA ?

Does anyone know of other tools(websites,programs,books) i may
    find useful ?

Should I drop this project until the tools are available to deal with
    repetitive DNA ?

Thank you very much for any help or suggestions.  I have exhausted
nearly all ofmy ideas, and have nobody from whom to recieve peer
review, and discuss this project.   Curt responses pointing me to FAQs,
websites,jounals etc are fine.  


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