Simultaneous Alignment and Folding of Protein Sequences

9 years 6 months ago
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...
Bonnie Berger, Charles W. O'Donnell, Jér&oc
Added 23 Nov 2009
Updated 23 Nov 2009
Type Conference
Year 2009
Authors Bonnie Berger, Charles W. O'Donnell, Jérôme Waldispühl, Rolf Backofen, Sebastian Will, Srinivas Devadas
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