Re: [modeller_usage] Fwd: SALIGN

On 6/11/10 6:00 PM, Piyush Diyora wrote: >> I performed multiple sequence alignment using salign. When I >> analysed the result output (.pap output), there was some improper >> alignment at 400th position.

If you think you know what the alignment should look like at the 400th position, you can offset the dynamic programming matrix to force it. See http://salilab.org/modeller/9v8/manual/node294.html#SECTION00111525600000000... for an example.

Ben Webb, Modeller Caretaker