[phenixbb] sculptor : "Wrong alignment format:"

[Bryan Lepore]

On Mon, Nov 29, 2010 at 6:36 AM, Dr G. Bunkoczi <gb360 at cam.ac.uk> wrote:
>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