title: Software Suite for Gene and Protein Annotation Prediction and Similarity Search.
abstract: In the computational biology community, machine learning algorithms are key instruments for many applications, including the prediction of gene-functions based upon the available biomolecular annotations. Additionally, they may also be employed to compute similarity between genes or proteins. Here, we describe and discuss a software suite we developed to implement and make publicly available some of such prediction methods and a computational technique based upon Latent Semantic Indexing (LSI), which leverages both inferred and available annotations to search for semantically similar genes. The suite consists of three components. BioAnnotationPredictor is a computational software module to predict new gene-functions based upon Singular Value Decomposition of available annotations. SimilBio is a Web module that leverages annotations available or predicted by BioAnnotationPredictor to discover similarities between genes via LSI. The suite includes also SemSim, a new Web service built upon these modules to allow accessing them programmatically. We integrated SemSim in the Bio Search Computing framework (http://www.bioinformatics.deib. polimi.it/bio-seco/seco/), where users can exploit the Search Computing technology to run multi-topic complex queries on multiple integrated Web services. Accordingly, researchers may obtain ranked answers involving the computation of the functional similarity between genes in support of biomedical knowledge discovery.
authors.forename: Davide
authors.initials: D
authors.lastname: Chicco
authors.forename: Marco
authors.initials: M
authors.lastname: Masseroli
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D000069550:Machine Learning; D058977:Molecular Sequence Annotation / Q000379:methods*; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012660:Semantics; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins