Re: [Seqan-dev] Best index for task
Hi John,
you should definitely try the Wotd-algorithm if you do a pruned search.
We have had huge improvement over the ESA for different problems in
terms of memory and running time using the Wotd, especially if your
working on a range of suffix lengths where it is more technical to
employ Q-gram indices.
Also, the pruning with the Wotd-Algorithm is very effective if you work
on large alphabets, like proteins.
Bests,
Marcel
Am 22.03.11 06:50, schrieb John Reid:
Hi,
I have a motif search algorithm I have coded using a enhanced suffix
array. I'm wondering if its worth investigating other indexes to see
if they are more efficient. The algorithm builds an index over a sets
of sequences, say 5Mb average total size. My algorithm descends the
index to a given maximum depth (say 20 bases) many times but never
goes deeper. It doesn't descend all paths, it does some pruning on the
way down. Up until now I have been using the IndexEsa. I notice I
could also use the IndexWotd, the IndexQGram or perhaps something from
Pizza&Chili. Has anyone got any recommendations about what might be
quickest for this sort of task? I realise I haven't given you too much
to go on but perhaps it is enough without describing the algorithm in
full. My code compiles with either the IndexWotd or the IndexEsa but
with IndexQGram I get compilation errors. Should these indexes have
the same programming interface?
Thanks for a great library,
John.
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev
--
------------------------------------------------------------------------------
Marcel H. Schulz
Ray and Stephanie Lane Center email: maschulz@cs.cmu.edu
for Computational Biology
Carnegie Mellon University
7413 Gates-Hillman Complex
5000 Forbes Avenue
Pittsburgh, PA 15213
http://www.cs.cmu.edu/~maschulz/
------------------------------------------------------------------------------
