On Jun 14, 2009, at 7:49 PM, C. Titus Brown wrote: > -> 2. handling of self-alignment in pairwise mode. We proposed > changing > -> pairwise mode to report self-alignments, rendering obsolete the > -> current annoying warning message. > > +1, will submit patch this week.
I may have missed it, but did you ever submit this patch? > > -> 3. blastx 6 frame ORFs. We proposed changing this so each sequence > -> would have just 6 full-length ORFs associated with it, and > therefore > -> blastx could return a single NLMSA (containing all the results), > just > -> as the regular blastn/blastp mode does. > > +1, working on details. I'm going to try to summarize what I thought you were proposing: - switch blastx etc. to use "canonical" TranslationAnnot that cover the entire sequence (i.e. six different frames). Presumably this requires a naming convention for these annotations, based on seqID and frame. Another required change: need to "translate" STOP codons, presumably to * - blastx would report results ito slices of these canonical annotations, just as blastn etc do, i.e. by saving all results to a single NLMSA. - blastx __call__ and __getitem__ interface would become just like standard blastn behavior, i.e. __call__ returns NLMSA. I liked your proposal in part because it could greatly simplify the blastx handling. In fact, it may not be necessary to have separate code for blastx at all, since the interface and results would be essentially the same as standard blastn handling. I think one new class could greatly simplify this whole setup: it would mirror a nucleotide sequence database, but return slices of TranslationAnnot representing the protein. We would pass this as the "query sequence database" instead of the nucleotide sequence database. I guess I will try creating an experimental branch based on this idea... -- Chris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
