[Biococoa-dev] starting BCAlignment

Alexander Griekspoor a.griekspoor at nki.nl
Thu Mar 10 16:41:28 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...

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)
          Plesmanlaan 121, 1066 CX, Amsterdam
                    Tel:  + 31 20 - 512 2023
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                  E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

               4Peaks - For Peaks, Four Peaks.
        2004 Winner of the Apple Design Awards
                Best Mac OS X Student Product


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