[Biojava-l] Interested in the "cloudization" of BioJava

[Andreas Prlic]

Hi Arthur,

> 1) The first one and the one i find most interesting can be to try to
> introduce the map-reduce framework to help to speed-up the pairwise
> alignment in the creation of the muliple sequence alignment.

That would be a possible application.

> 2)If the input files are big enough, it can be interesting to perform the
> parsing on this files while using a distributed infrastructure to speedup
> the process,

I am not sure if I have encountered such large files as of yet. Do you
have an example?

> 3)Another idea can be to try to have a hadoopify version of blast, in which
> the input file also can be splitted and then for each sequence in a chunk,
> the node would perform a local blast query.

I agree, another possible application...

What frameworks did you think about using?

Andreas