[Biococoa-dev] starting BCAlignment

Philipp Seibel biococoa at bioworxx.com
Thu Mar 10 16:50:13 EST 2005

> I can ;-)
> Actually for 4Peaks I use a global alignment which 1) doesn't 
> penaltize beginning and end gaps (almost making it local), 2) doesn't 
> penalitize extra above a certain gap length (meaning that introns in 
> your sequences don't end up with huge penalties).... 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 ;-).

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


> 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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