[phenixbb] sculptor

Bryan Lepore bryanlepore at gmail.com
Fri Nov 19 08:23:31 PST 2010

On Fri, Nov 19, 2010 at 5:16 AM, Dr G. Bunkoczi <gb360 at cam.ac.uk> wrote:
> Would it be sufficient to provide
> an option, so that one can specify the index of the target sequence in the
> alignment file?

in the interest of automation, i guess - though the titles (the stuff
on the line starting with ">") can get pretty disgusting if you keep
everything from the database it came from : non-alphabetic characters,

>Would it be better to provide the target sequence, and let
> Sculptor figure out the index itself?

can't say if its better, but if it works - why not.

i have seen programs where you say e.g. "fubar" and then the alignment
has a part with ">fubar" then everything between ">fubar" and the next
">" is defined as the target sequence (IIUC).

... anyways, how is the target sequence used that a consensus sequence
couldn't be used instead? i mean, the model looks like it has one
applied to it.


More information about the phenixbb mailing list