[Bioperl-l] Scoring an overlap

Florent Angly florent.angly at gmail.com
Sat Sep 22 21:41:40 EDT 2007

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 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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