Simultaneous Alignment and Folding of Protein Sequences

Abstract. Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFoldAlign, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane -barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments, partiFold-Align significantly outperforms state-of-the-art pairwise sequence alignment tools in the most difficult low sequence homology case and improves secondary st...

• Type: Conference
• Year: 2009
• Where: RECOMB
• Authors: Bonnie Berger, Charles W. O'Donnell, Jérôme Waldispühl, Rolf Backofen, Sebastian Will, Srinivas Devadas
• Keywords: Computational Biology, Difficult Low Sequence, Pairwise Sequence Alignment, RECOMB 2009, Simultaneous Pairwise Alignment