[Bioperl-l] Scoring an overlap

Chris Fields cjfields at uiuc.edu
Mon Sep 24 14:11:47 EDT 2007


As Chad mentioned it could be a stack issue, but it might be worth  
filing a bug on.  I will note that bioperl-ext has seen very little  
use in the last few years, so don't expect it to be fixed unless you  
can contact the ext module author.

chris

On Sep 22, 2007, at 8:41 PM, Florent Angly wrote:

> Eventually, I gave Bio::Tools::dpAlign a try. I had no luck running it
> when installing its dependency, bioperl-ext v1.4 or v1.5.1. However  
> all
> the tests passed when installing the CVS version.
> So finally, here I am trying to score my alignments. For alignments  
> of 2
> small sequences, it works, but as soon as the sequences get bigger  
> than
> a few dozen nucleotides, it crashes:
> Segmentation fault (core dumped)
>
> I did not find any help in the documentation...
>
> Can I fix this? Is this a bug?
>
> Thanks for your help,
>
> Florent
>
> Florent Angly wrote:
>> Hi,
>> I need to quantify how good some overlaps in contigs are. I have
>> extracted the alignment of the overlapping region and only need to
>> score it. I noticed the Bio::Tools::dpAlign has a scoring function.
>> Is it the right tool for the right tool? Is there anything else?
>> Thank you,
>> Florent
>>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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