Volkan Atalay1, Rengul Cetin-Atalay. 1. Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
Abstract
MOTIVATION: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive. RESULTS: A system named P2SL that infer protein subcellular targeting was developed through this computational kernel. Targeting-signal was modeled by the distribution of subsequence occurrences (implicit motifs) using self-organizing maps. The boundaries among the classes were then determined with a set of support vector machines. P2SL hybrid computational system achieved approximately 81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes. P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol. AVAILABILITY: http://staff.vbi.vt.edu/volkan/p2sl and http://www.i-cancer.fen.bilkent.edu.tr/p2sl CONTACT: rengul@bilkent.edu.tr.
MOTIVATION: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive. RESULTS: A system named P2SL that infer protein subcellular targeting was developed through this computational kernel. Targeting-signal was modeled by the distribution of subsequence occurrences (implicit motifs) using self-organizing maps. The boundaries among the classes were then determined with a set of support vector machines. P2SL hybrid computational system achieved approximately 81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes. P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol. AVAILABILITY: http://staff.vbi.vt.edu/volkan/p2sl and http://www.i-cancer.fen.bilkent.edu.tr/p2sl CONTACT: rengul@bilkent.edu.tr.