MSP

[rmhubley]

Are there any plans to implement a multiple high scoring pairs ( MSP ) version of your algorithms? Perhaps its there and I don't see the options to invoke it. Instead of the highest scoring alignments I want all high scoring ( above a given score threshold ) of the query against a long sequence.

[jeffdaily]

Chances are low that I could get to a feature like this, but there is some hope since this feature might not take too much effort to implement. Is there some example output from another application that provides what you're wanting? That said, any parasail alignment that contains traceback information will contain everything you need in order to ask for multiple pairwise solutions. Currently, the parasail alignment result only tracks the sequence endpoints from the two sequences for the best solution, but the traceback function only needs to know where to start from, so in theory we could just re-use that function with other starting locations.

Clarifying, I am assuming this use case is only for local alignments? It doesn't make sense for global and semi-global.