[Seqan-dev] FM-Index help

["Singer, Jochen" <Jochen.Singer@fu-berlin.de>]

Hi Robert,

the FM-Index is a collection of tables which are based on SeqAn's Alloc Strings (in the end). These strings are kept in memory and not on the disc. Therefore I am a little puzzled by the running times. Could you provide the code and an example file, or a demo showing you problem?

Kind regards,

Jochen

Hello,

I was able to create, save and open the FM-Index for the swiss-prot database (its size is around 250MB). Does the open function store the complete index to the working memory or does it read from the created files when needed? If the answer is the latter, could you please explain me how can I store the index to working memory or speed up searching in any way? The database has 315 queries and I am searching the index for each subsequence of 5 amino acids (in query proteins) which results in 178 seconds which is too much (say the average length of proteins is 1300, I have around (1300 - 4) * 315 searches with patterns of 5 letters).

Thank you!

Jochen Singer
Institute of Computer Science

Algorithmic Bioinformatics Working Group

Freie Universität Berlin
Takustr. 9, 14195 Berlin
Phone +49 30 838 75228, Room K25