Regarding Needleman Winsch global genome alignment using nvbio

[Muhammad Mobeen Movania]

Can we do global genome sequence alignment using NW algoritm with nvbio ? I see it mentioned here ( https://rmcsoftwareinc.wordpress.com/2014/12/25/nvbio-gpu-accelerated-bioinformatics-library/ ) but the nvbio distribution does not contain one. So my question is
1) is is possible with nvbio?
2) if not given with nvbio, what are the best sources to learn and implement NW in nvbio?
3) if not possible in nvbio, what are the alternate libraries that implement NW in CUDA?

Thanks,
Mobeen

[Jacopo Pantaleoni]

Hi Muhammad,

NW is essentially Smith-Waterman with the GLOBAL (or SEMI_GLOBAL) alignment tag. So you can use that on the GPU if you need to solve many independent short paired alignments (e.g. many thousands or millions of short alignments with up to ~2K bps per string) that can be run in parallel. If you need to align only two or a few very long strings against each other we don't yet have explicit GPU support for it, though it should be possible to craft it using the per-warp implementation, assigning one warp per matrix block and processing blocks in wavefronts parallel to the anti-diagonal (saving the borders in global memory for communication across blocks).

Let me know if you have any more questions.

-jacopo

--
You received this message because you are subscribed to the Google Groups "nvbio-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nvbio-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Muhammad Mobeen Movania]

Thanks Jacopo for a prompt reply.