On Mon, Nov 29, 2010 at 6:36 AM, Dr G. Bunkoczi
On my machine, searching a 190-sequence alignment takes about 5 mins. (time output didn't make it for some reason).
reading ahead in the email, so i just tried dev-592, still takes a very long time. i finally understand that sculptor is in fact calculating an alignment. my alignments have been pre-aligned (mafft usually). i have not tried a .def to turn off the alignment - can i do that?
what you are trying the achieve with using such a large alignment....you must be trying to extract as much information from the sequence alignment as possible,
yes
I am not sure the sequence similarity calculation as implemented in sculptor is optimal for this
i see
Could you also give some advice on how this is best calculated?
in terms of algorithms out there, IIUC mafft has a very sophisticated algorithm for it, and at any rate it can be compiled with multithreading. its license appears not to be prohibitive. -Bryan