On Mon, Jun 29, 2009 at 12:13:46PM +0900, Namshin Kim wrote: -> I will make AnnotationDB later, but for the variation analysis, in order to -> save sequence information, I prefer pairwise NLMSA only for the nucleotides -> that has been changed during sequencing. It would be better to have only one -> NLMSA, but I rather choose to have two NLMSA (AnnotationDB & pairwise NLMSA) -> for now. AnnotationDB for coverage and gene analysis and pairwise NLMSA for -> variation analysis. -> Do you think it is a good idea? I agree that it is kind of inelegant to have -> two NLMSA... But I was afraid that the input files will be very big...
I think that's how I'm going to be doing it myself (one NLMSA for alignment, others for annotations). You might be interested to know that a student is working on an NLMSA-like interface specifically for short-read alignments, too; we should have a prototype within a few weeks. The goal is to have an NLMSA-compatible interface for the basic storage. (It will likely come to a more immediately useful resting point than screed, which is not being worked on much over the summer while Alex is gone.) cheers, --t --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
