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Updated: May 20, 2026

Pattern-based Search of Epigenomic Data Using GeNemo
Published on: October 8, 2017
Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences
Madhavi K Ganapathiraju1, Asia D Mitchell, Mohamed Thahir
1Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Boulevard, Suite BAUM 423, Pittsburgh, PA 15206-3701, USA. madhaviþblmt@pitt.edu
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.
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