protein consensus - (Jun/27/2006 )

Hy to everyone,
I want to use a program call "consensus" find at:

http://coot.embl.de/Alignment/consensus.html

this program it's very good for me, but I can't modify the parameter "grouping" of proteins.

Someone can Help me?

Sorry for my "spaghetti" english!!!!
Marco. [size=2]

-zealotto-

Why on earth do you want to modify the grouping of the acids?
It looks as if there are problems beyond you control if you are trying to add groups (object not found error)... If you need this facility (I can't imagine why) then email the fine people at EMBL.

Alternativly you (a bioinformatics group/person) could hash together a script (in say perl! ) to do the job for you.

-perlmunky-

Because there are too many group and... you can't see a information... very well...
Have you ever done with multialignament?
anyway, thanks for your reply

PS: I WANT LEARN PEARL!

-zealotto-

I am not sure I follow! There are the typical amino acid groups (pure positions) totally mixed, hydrophobic/philic & aromatic etc (see Taylor's Venn Diagram for a full breakdown). If your main aim is to create a consensus sequence from the MSA then why don't you take a look at 'cons' a prgram from the emboss package.

Oh it's perl by the way not PEARL.

-perlmunky-

Ok, thanks for your help...
but I have a Txt file... no .msf...

AND...sorry for PERL!!!!!!!

-zealotto-

can you post your text file with a little explanation as to whats in it.

TTFN

-perlmunky-

I have contacted the Webmaster: Dr.Yan P. Yuan and now the program Consensus works very well!!!
Remember to all:
the grouping of protein MUST be modify.... because K,R aren't hydrofobic protein!
Bye.
Marco

-zealotto-