Dataset Information

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.

ABSTRACT:

Background

Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we present INDUS - a composition-based approach that incorporates the following novel features. First, INDUS discards the 'one genome-one composition' model adopted by existing compositional approaches. Second, INDUS uses 'compositional distance' information for identifying appropriate assignment levels. Third, INDUS incorporates steps that attempt to reduce biases due to database representation.

Results

INDUS is able to rapidly classify sequences in both simulated and real metagenomic sequence data sets with classification efficiency significantly higher than existing composition-based approaches. Although the classification efficiency of INDUS is observed to be comparable to those by similarity-based approaches, the binning time (as compared to alignment based approaches) is 23-33 times lower.

Conclusion

Given it's rapid execution time, and high levels of classification efficiency, INDUS is expected to be of immense interest to researchers working in metagenomics and microbial ecology.

Availability

A web-server for the INDUS algorithm is available at http://metagenomics.atc.tcs.com/INDUS/

SUBMITTER: Mohammed MH

PROVIDER: S-EPMC3333187 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

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Publications

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.

Mohammed Monzoorul Haque MH Ghosh Tarini Shankar TS Reddy Rachamalla Maheedhar RM Reddy Chennareddy Venkata Siva Kumar CV Singh Nitin Kumar NK Mande Sharmila S SS

BMC genomics 20111130

<h4>Background</h4>Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we pre ...[more]

PMID: 22369237

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Project description:BackgroundMicroRNAs (miRNAs) are endogenous ?22 nt RNAs that are identified in many species as powerful regulators of gene expressions. Experimental identification of miRNAs is still slow since miRNAs are difficult to isolate by cloning due to their low expression, low stability, tissue specificity and the high cost of the cloning procedure. Thus, computational identification of miRNAs from genomic sequences provide a valuable complement to cloning. Different approaches for identification of miRNAs have been proposed based on homology, thermodynamic parameters, and cross-species comparisons.ResultsThe present paper focuses on the integration of miRNA classifiers in a meta-classifier and the identification of miRNAs from metagenomic sequences collected from different environments. An ensemble of classifiers is proposed for miRNA hairpin prediction based on four well-known classifiers (Triplet SVM, Mipred, Virgo and EumiR), with non-identical features, and which have been trained on different data. Their decisions are combined using a single hidden layer neural network to increase the accuracy of the predictions. Our ensemble classifier achieved 89.3% accuracy, 82.2% f-measure, 74% sensitivity, 97% specificity, 92.5% precision and 88.2% negative predictive value when tested on real miRNA and pseudo sequence data. The area under the receiver operating characteristic curve of our classifier is 0.9 which represents a high performance index.The proposed classifier yields a significant performance improvement relative to Triplet-SVM, Virgo and EumiR and a minor refinement over MiPred.The developed ensemble classifier is used for miRNA prediction in mine drainage, groundwater and marine metagenomic sequences downloaded from the NCBI sequence reed archive. By consulting the miRBase repository, 179 miRNAs have been identified as highly probable miRNAs. Our new approach could thus be used for mining metagenomic sequences and finding new and homologous miRNAs.ConclusionsThe paper investigates a computational tool for miRNA prediction in genomic or metagenomic data. It has been applied on three metagenomic samples from different environments (mine drainage, groundwater and marine metagenomic sequences). The prediction results provide a set of extremely potential miRNA hairpins for cloning prediction methods. Among the ensemble prediction obtained results there are pre-miRNA candidates that have been validated using miRbase while they have not been recognized by some of the base classifiers.

Dataset Information

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.

Background

Results

Conclusion

Availability

Publications

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.

Similar Datasets

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