Chris, I have a request or suggestion for you -- how about writing some short doctest-style descriptions of how you would work with blastn, blastx, tblastn, tblastx, and blastp results, as discussed below? Seeing code that describes these interactions might help me give input on possible alternatives.
Just a thought... cheers, --titus ----- Forwarded message from [email protected] ----- Comment #2 on issue 44 by cjlee112: tblastn and blastx support http://code.google.com/p/pygr/issues/detail?id=44 tblastn case is simplest: - protein query vs. nucleotide db, returned as protein-protein alignments - for each hit, just consolidate all the subject intervals into a single ORF annotation (TranslationAnnot), and save the alignment of the query protein to slices of the TranslationAnnot. - user accesses the alignment results as usual, but gets one added feature: the aligned protein intervals have a sequence attribute that yields the associated nucleotide sequence interval from the nucleotide database. Simple, clean. By contrast, blastx poses some hard problems, because we no longer have *one* query sequence as our alignment interface naturally assumes. The query sequence might be represented by any number of different ORFs, some of which might show up in many individual blast hits. It's not clear whether users will want these to be reported as one sequence or different sequences (this is especially tricky if you have non-overlapping intervals of a common ORF). Maybe I should just give blastx a different interface, one that just follows BLAST's interface: a list of hits. That could be quite simple: for each hit just follow the same recipe above of consolidating into one annotation and reporting aligned slices vs. subject database sequence slices. Actually tblastx could also be done as a hybrid of the blastx + tblastn solutions I proposed above. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings ----- End forwarded message ----- -- C. Titus Brown, [email protected] --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
