On Wed, Jul 15, 2009 at 09:49:57PM -0700, Christopher Lee wrote: -> I just posted a new branch "simpleframe" on github, which implements -> everything we've been discussing for simplifying blastx etc. It -> drastically simplifies the tblastn and blastx code. All the pipeline -> and transformations stuff is unnecessary now. I simply created a new -> "sequence database" class called TranslationDB that wraps a nucleotide -> sequence database and provides an interface to six-frame translations -> of the nucleotide sequences as you had suggested. That means that -> blastx / tblastn / tblastx are processed exactly the same as blastn / -> blastp (they just substitute a TranslationDB for the source and / or -> target sequence databases). All blastx results are now stored in a -> single NLMSA, rather than being divided into a separate NLMSA / -> NLMSASlice for each hit as before.
OK -- the changes look good, on a cursory reading. I'm not sure I understand all the implications yet, but it certainly simplified the BLAST code, which is a great sign! One of the things I wanted to do with my code was to provide a 'translation' on sequences that would let you translate a DNA sequence into a protein sequence in any specified frame. What do you think? --titus -- 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 -~----------~----~----~----~------~----~------~--~---
