On Sat, Jun 13, 2009 at 08:54:54PM -0700, Christopher Lee wrote: -> First, I've noticed with increasing alarm that BLAST is like a black -> hole that will suck in more and more development effort seemingly -> without limit.
[ ... ] Yup ;) -> I would rather achieve "80% of the value for 20% of the effort" by -> drawing a clear line separating what we will vs will not do for BLAST, [ ... ] Sounds good. -> 1. the BLAST path whitespace bug. The BLASTDB env variable only works -> for blastall, not for formatdb, so it doesn't really solve the problem -> for us. So I think we should just raise a clear error message telling -> the user that BLAST can't handle whitespace in file paths. +1 -> 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. -> 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. cheers, --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 -~----------~----~----~----~------~----~------~--~---
