salign multiple structures, with an initial multiple sequence alignment
Hi Modellers,
Trying to align several structures of a similar domain, I have a "hand-made" sequence alignment for these domains. Is it possible to ask salign to use this initial sequence alignment ? Is it possible to ask salign to keep that same multiple sequence alignment unchanged during the whole process ?
thanks
--Ben.S
On 4/7/11 9:20 AM, Benjamin SCHWARZ wrote: > Trying to align several structures of a similar domain, I have a > "hand-made" sequence alignment for these domains. Is it possible to > ask salign to use this initial sequence alignment ? Is it possible to > ask salign to keep that same multiple sequence alignment unchanged > during the whole process ?
If you don't want to change the alignment, then there's not really a "process" going on here (since the "process" is optimizing the alignment by means of dynamic programming). It sounds like what you want to do is superpose several structures based on an existing sequence alignment. You want superpose(), not salign(). Note that superpose is only pairwise though, so you'll have to run it in a loop.
Ben Webb, Modeller Caretaker
> If you don't want to change the alignment, then there's not really a "process" going on here (since the "process" is optimizing the alignment by means of dynamic programming). It sounds like what you want to do is superpose several structures based on an existing sequence alignment. You want superpose(), not salign(). Note that superpose is only pairwise though, so you'll have to run it in a loop. > > Ben Webb, Modeller Caretaker
I clearly understand now it makes no sense to fix the alignment once and forall, since the principle of the optimization algorithm indeed relies on its modification :-) Still, would it make sense to feed salign with an initial "hand-made" alignment ? If so, is it possible and how to do it ?
Thanks also for the clarification of concepts between alignment and superposition. As for the superpose() method you pointed out, I guess it is the one from class selection since I see no other occurrence of the "superpose" token in the doc.
--Ben.S
On 4/8/11 8:15 AM, Benjamin SCHWARZ wrote: > I clearly understand now it makes no sense to fix the alignment once > and forall, since the principle of the optimization algorithm indeed > relies on its modification :-) Still, would it make sense to feed > salign with an initial "hand-made" alignment ? If so, is it possible > and how to do it ?
Of course - whatever alignment you have when you run SALIGN is used as its initial alignment.
> Thanks also for the clarification of concepts between alignment and > superposition. As for the superpose() method you pointed out, I guess > it is the one from class selection since I see no other occurrence of > the "superpose" token in the doc.
Yes, that's the one.
Ben Webb, Modeller Caretaker
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Modeller Caretaker