Uses dynamic programming schemes to simultaneously list the complete space of structures and sequence alignments and compute the optimal solution. PartiFold-Align is an algorithm for simultaneous alignment and folding pairs of unaligned protein sequences. This tool exploits scarcity in the set of super-secondary structure pairings and alignment candidates to attain an effectively cubic running time. It also get better secondary structure prediction where current approaches fail.
School of Computer Science, McGill University, Montreal, Canada; Departments of Mathematics, Computer Science and AI Lab, and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut fur Informatik, Albert-Ludwigs-Universitat, Freiburg, Germany; Department of Computer Science and IZBI, University of Leipzig, Leipzig, Germany