Madhavi Ganapathiraju

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BACKGROUND Prediction of transmembrane (TM) helices by statistical methods suffers from lack of sufficient training data. Current best methods use hundreds or even thousands of free parameters in their models which are tuned to fit the little data available for training. Further, they are often restricted to the generally accepted topology(More)
— Telugu is an Indian language spoken by over 50 million people in the country. The language is rich in literature and has been studied by native and foreign linguists significantly, yet it has not benefited significantly from the recent advances in computational approaches for linguistic or statistical processing of natural language texts. However with the(More)
UNLABELLED TMpro is a transmembrane (TM) helix prediction algorithm that uses language processing methodology for TM segment identification. It is primarily based on the analysis of statistical distributions of properties of amino acids in transmembrane segments. This article describes the availability of TMpro on the internet via a web interface. The key(More)
Statistical analysis of amino acid and nucleotide sequences, especially sequence alignment, is one of Abstract the most commonly performed tasks in modern molecular biology. However, for many tasks in bioinformatics, the requirement for the features in an alignment to be consecutive is restrictive and 'n-grams' (aka k-tuples) have been used as features(More)
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(More)
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