PSSPred Alignment Alignment

Question

[virpatel3]

PSSPred gives me wonderful data of protein secondary structures. For instance, I have

HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCHHHHHHHH

for one part of my prediction. I want to perform an alignment with this data, but I am quite unsure as to what would be the best algorithm. Any suggestions?

[Ram]

"Perform an alignment" is as vague as it can get. What do you wish to align? The secondary structure? What do you wish to align it to? A sequence? Another secondary structure? And what are you looking to achieve with this?