Re: [boost] Bioinformatics algorithms in boost?

From: Robert Goldwein (robert.goldwein_at_[hidden])
Date: 2006-12-05 12:47:06

Dear Johan,

thanks for your reply - so you surely know about bioinformatics frameworks for Perl or Python, and I miss something good in C++ (I found several bioinformatics projects, or FASTA and BLAST implementations, but my idea is a general multipurpose library).

You are right, problems like gene prediction or algorithms like BLAST are quite specific, but it all uses general string algorithms. Maybe it would be wiser to divide it into some advanced string library and specialized bioinformatics library, but on the other hand, those string algorithms can be optimized specifically for our specific conditions (triplets, limited set of characters, etc.)... In about a month I should have some sketch, so I'll let you know.

Thanks for encouraging words,
Robert

 

-----Original Message-----
From: boost-bounces_at_[hidden] [mailto:boost-bounces_at_[hidden]] On Behalf Of Johan Råde
Sent: Tuesday, December 05, 2006 15:28
To: boost_at_[hidden]
Subject: Re: [boost] Bioinformatics algorithms in boost?

Robert Goldwein wrote:
> Hello all,
> 
> for my thesis, I'll be developing a self-contained framework for
> algorithms used in bioinformatics. This will include algorithms such as
> Hamming distance, Levenshtein distance or Longest common subsequence
> algorithms, gene prediction algorithms, 2D and 3D scoring matrices,
> alignment problems, etc.
> 
> Would be there - in some near future - any interest in such library?
> 
> Thanks,
> R. Goldwein
> _______________________________________________
> Unsubscribe & other changes: http://lists.boost.org/mailman/listinfo.cgi/boost
> 

Dear Robert,

I'm working in bioinformatics,
so I would be very interested in your library.
A good and free bioinformatics library should be very useful.
It sounds like a great initiative.

However, I also think it may be a bit too domain-specific to belong to 
Boost.

--Johan

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