[Biococoa-dev] starting BCAlignment

Alexander Griekspoor a.griekspoor at nki.nl
Thu Mar 10 16:54:56 EST 2005

>> A nice example where you pick a certain alignment algorithm for a 
>> certain situation simply because it's the best fit. In general one 
>> algorithm isn't better per se than the other, often they're just 
>> suited for different situations...
>> Alex
> Seems to grow up into an alignment battle between me and you LOL ;-).
No, please no, that was exactly what I didn't want to do.... sorry for 
that. The last sentence was purely informative for the others, without 
any offensive ideas towards your plans.
> I want to start coding with the BCNeedlemanWunsch, but i'm not sure 
> whether i should put it into my BCAlignments folder or in the BCTools 
> folder. I would prefer the BCAlignment folder. What do you think
I think you're right, it would be nice to keep everything alignment in 
the BCAlignment folder. In fact I'm not even sure if we even need a 
tool by smart use of class methods, but time will tell...

>> On 10-mrt-05, at 22:23, Philipp Seibel wrote:
>>> The piece of code alex just sent arround is great to understand what 
>>> a global alignment is. Alex uses two types of scores, a match and a 
>>> mismatch score, this is the simplest way to align sequences. It 
>>> produces quite good alignments for dna sequences, but in the most 
>>> common cases, you need the scoring matrix to score different kind of 
>>> matches and mismatches. Another point is to differentiate between 
>>> gap-open and gap-extension costs, but this is more relevant at local 
>>> alignments.
>>> Ok i stop here, because nobody can follow me anymore ..... ;-)
>>> Phil
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                     ** Alexander Griekspoor **
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
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                     E-mail: a.griekspoor at nki.nl
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