Hi,
I was wondering if one could use an external multiple sequence alignment (instead of align2d or equivalent functions) with modeller and how I could go about doing that. Thanks for any help you could provide.
Ashika,
On 9/4/14, 5:04 AM, ashika torikora wrote: > I was wondering if one could use an external multiple sequence alignment > (instead of align2d or equivalent functions) with modeller and how I > could go about doing that. Thanks for any help you could provide.
Sure - you don't have to do anything special. You just need to make sure the alignment is in the PIR format that Modeller understands.
Ben Webb, Modeller Caretaker
Ashika,
Just to expand on what Ben said, you can use any tool to generate the alignment. Converting it into PIR format can be done with a number of programs- I have used Jalview (see jalview.org) for example.
However, you will still need to do some editing of the .pir file for Modeller to read it. The first two lines of each sequence entry need to correspond to the description in the manual: https://salilab.org/modeller/manual/node494.html#alignmentformat
Hope that helps, -Jonathan
-
ashika torikora -
Jonathan Sheehan -
Modeller Caretaker