Re: [Seqan-dev] Best index for task

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Am 22.03.2011 um 11:50 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?

Wotd is a lazy suffix tree which might be better for your algorithm. It should serve as a drop-in-replacement for Esa if you are using iterators.

I don't know if IndexQGram helps you much since it's a classical q-gram index/lookup table.

HTH