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...
Namshin Kim On Mon, Jun 29, 2009 at 12:06 PM, C. Titus Brown <[email protected]> wrote: > > On Mon, Jun 29, 2009 at 11:20:53AM +0900, Namshin Kim wrote: > -> No. I am building pairwise NLMSA from custom-made axtNet files. axtFiles > are > -> not that big but there are 14m sequences in it. It would take 2-3 hours > for > -> pygr to make .idDict and .seqIDdict. > > ahh, I see. is that how you'd recommend doing this sort of thing, then? > transforming the input first? seems kind of inelegant... > > --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 -~----------~----~----~----~------~----~------~--~---
