[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...
Alex
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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>
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** Alexander Griekspoor **
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The Netherlands Cancer Institute
Department of Tumorbiology (H4)
Plesmanlaan 121, 1066 CX, Amsterdam
Tel: + 31 20 - 512 2023
Fax: + 31 20 - 512 2029
AIM: mekentosj at mac.com
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
http://www.mekentosj.com/4peaks
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