protein sequence generation

Frank Fürst frank at fuerst.de
Thu Mar 25 15:09:46 EST 1999


Hi,

Andy Phillips wrote:
> 
> Cornelius Krasel wrote:
> >
> > Be aware that for a protein with n
> > residues there are approximately n! different sequences (somewhat
> > less because of repetitions).
> >
> 
> Err..shouldn't that be 20^n (20 to the nth power) different sequences??

You're right. But on the other hand, if we come back to the original
question (which I snipped out above...), even with a molecular weight
tolerance of +- zero, one gets n! different sequences. Plus the
sequences with multiple mutations that compensate each other, each of
them again n! times. So n! gets somewhat important, because for every
sequence a man would find calculating with his pencil, the computer
would find n!

Maybe Peter Hufnagel should explain for what purpose he wants to use
these sequences. Perhaps than we could find a way to restrict the
combinatorial search to only useful solutions?

Frank


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