[Biococoa-dev] BCPairwiseAlignment & BCScoreMatrix
Koen van der Drift
kvddrift at earthlink.net
Fri Mar 11 19:46:12 EST 2005
Another ignorant question:
what's the difference between alignment and pairwise alignment?
Regarding their place in BioCocoa, should BCPairwiseAlignment be a
subclass of BCAlignment? Right now it isn't, although I would expect
that based on their names.
- Koen.
On Mar 11, 2005, at 4:31 PM, Alexander Griekspoor wrote:
>
> On 11-mrt-05, at 17:47, Philipp Seibel wrote:
>
>> Hi everybody,
>>
>> i just made some modifications to the Alignment stuff. I followed
>> Alex' advice and made the Scoring Matrix char based. every symbol is
>> casted to a char and used as a number key for the matrix. With this
>> approach we have some memory overhead, but we're much faster, because
>> we need not to ask the NSArray for the Symbol index everytime.
>>
>> I also copied some of alex' code ( sorry for that alex ;-) ) to
>> provide a short overview over the global alignment.
> Absolutely no problem!
> Just to make things clear for everyone, with alignments we're talking
> about two kinds of matrices. The one with the scores one which are
> also known as substitution matrices, although you can implement them
> as arrays as well like phil demonstrated before.
> These are different from the matrices used during the actual
> alignments (with the 3 phases as you might remember). For the first we
> create the scoring matrix objects, the second are probably only used
> internally in the algorithm implementation.
>
> So Koen, in this light your remark:
>> I am thinking how this will be used. The end user probably wants to
>> try out one type of alignment, see the result, then try another one,
>> compare the results, etc. So if we make a BCNeedlemanWunsch, and then
>> a BCSmithWaterman where is the actual matrix that is used to
>> calculate. I think it is a good idea if we have just one matrix, that
>> is used as a basis for each different calculation. It would be a
>> waste if for every calculation the starting matrix has to be
>> re-calculated. Or maybe that's where BCMatrix comes in place?
> The actual matrix used for calculation is the second one. But keeping
> the matrix only saves you the memory allocation, but different
> alignments fill the matrix differently so there's no use in keeping it
> around as it has to be refilled again with scores based on algorithm,
> penalty scores, gap costs etc. As most time goes into filling the
> matrix and tracing it back after the fill, you can't reuse it. Also,
> most algorithms that are subquadratic for memory requirements, chop up
> the matrix and use a divide-and-conquer approach because it's the
> storage of a complete-sized matrix that forms the memory problem.
> Does this make any sense?
> Alex
>
>>
>> @Charles: Perhaps we could discuss your symbol to int mapping in more
>> detail, i didn't get the idea. ;-)
>>
>> Phil
>>
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>>
>>
> *********************************************************
> ** Alexander Griekspoor **
> *********************************************************
> 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
>
> *********************************************************
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
More information about the Biococoa-dev
mailing list