[Biococoa-dev] testing alignements

[Alexander Griekspoor]

> I profiled the code in Shark (on my old iMac G3 400), and found it 
> spends ~35% of the time reading the score matrix. I don't know if it 
> is worth changing the char mapping to find if things are improved? 
> What do you think, guys?

I would say that depends on a number of things I guess. Let me explain:
- how well is the code performing right now? Is it slow?
- is this the only major part the code spends it time in and the rest 
is fragmented? Then yes, if there's something else where the algorithm 
stays 50% of the time in, I would first focus on that process
- are there real reasons to believe that remapping will significantly 
speed up things, then it's worth trying (don't forget to take the time 
remapping takes into account for a fair comparison)
- finally and perhaps most important, how much would remapping help in 
other implementations. Don't wanna sound to picky but although very 
nice, the current algorithms we have still have the classical memory 
limits. So if we can't run to large alignments because we run out of 
memory, why spend all the energy in optimizing speed instead of 
implementing an algorithm with subquadratic memory requirements? The 
real question then becomes, do we need the mapping there? Phil can 
probably tell...
Cheers,
Alex

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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

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