[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...
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
>>>
>>> _______________________________________________
>>> Biococoa-dev mailing list
>>> Biococoa-dev at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
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>
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** Alexander Griekspoor **
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The Netherlands Cancer Institute
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