[Seqan-dev] Best index for task

[John Reid <j.reid@mail.cryst.bbk.ac.uk>]

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.