title: Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences.
abstract: Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.
authors: Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Boulevard, Suite BAUM 423, Pittsburgh, PA 15206-3701, USA. madhaviþblmt@pitt.edu
authors: Madhavi K
authors: MK
authors: Ganapathiraju
authors: Asia D
authors: AD
authors: Mitchell
authors: Mohamed
authors: M
authors: Thahir
authors: Kamiya
authors: K
authors: Motwani
authors: Seshan
authors: S
authors: Ananthasubramanian
mesh_terms: D000465:Algorithms; D003627:Data Interpretation, Statistical; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods