Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines

Background: Conotoxin has been proven to be effective in drug design and could be used to treat various disorders such as schizophrenia, neuromuscular disorders and chronic pain. With the rapidly growing interest in conotoxin, accurate conotoxin superfamily classification tools are desirable to systematize the increasing number of newly discovered sequences and structures. However, despite the significance and extensive experimental investigations on conotoxin, those tools have not been intensively explored. Results: In this paper, we propose to consider suboptimal alignments of words with restricted length. We developed a scoring system based on local alignment partition functions, called free score. The scoring system plays the key role in the feature extraction step of support vector machine classification. In the classification of conotoxin proteins, our method, SVM-Freescore, features an improved sensitivity and specificity by approximately 5.864% and 3.76%, respectively, over pr...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Nazar Zaki, Stefan Wolfsheimer, Grégory Nuel, Sawsan Khuri
• Keywords: Biometrics, BMCBI 2011, Cone Snail, Suboptimal Alignments, Support Vector Machine