SUITE OF TOOLS FOR STATISTICAL N-GRAM LANGUAGE MODELING FOR PATTERN MINING IN WHOLE GENOME SEQUENCES-Reference-Cited by-同舟云学术

SUITE OF TOOLS FOR STATISTICAL N-GRAM LANGUAGE MODELING FOR PATTERN MINING IN WHOLE GENOME SEQUENCES

Published:2012-10-18 Issue:06 Volume:10 Page:1250016
ISSN:0219-7200
Container-title:Journal of Bioinformatics and Computational Biology
language:en
Short-container-title:J. Bioinform. Comput. Biol.

Author:

GANAPATHIRAJU MADHAVI K.¹,MITCHELL ASIA D.¹,THAHIR MOHAMED¹²,MOTWANI KAMIYA³,ANANTHASUBRAMANIAN SESHAN¹²

Affiliation:

1. Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Boulevard, Suite BAUM 423, Pittsburgh, PA 15206-3701, USA

2. Intelligent Systems Program, University of Pittsburgh, USA

3. Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India

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.

Publisher

World Scientific Pub Co Pte Lt

Subject

Computer Science Applications,Molecular Biology,Biochemistry

Link

https://www.worldscientific.com/doi/pdf/10.1142/S0219720012500163

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