[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
Phil
>
> 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
>>
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
More information about the Biococoa-dev
mailing list