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Title
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GSTaxClassifier: a genomic signature based taxonomic classifier for metagenomic data analysis
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Authors
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Fahong Yu$, Yijun SunS, Li Liu, William Farmerie | |
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Affiliation
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Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610; $ Equal contribution
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Article Type
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Hypothesis | |
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Date
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Received April 07, 2009; Accepted June 18, 2009; Published August 20, 2009 | |
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Abstract |
GSTaxClassifier (Genomic Signature based Taxonomic Classifier) is a program for metagenomics analysis of shotgun DNA sequences. The program includes (1) a simple but effective algorithm, a modification of the Bayesian method, to predict the most probable genomic origins of sequences at different taxonomical ranks, on the basis of genome databases; (2) a function to generate genomic profiles of reference sequences with tri-, tetra-, penta-, and hexa-nucleotide motifs for setting a user-defined database; (3) two different formats (tabular- and tree-based summaries) to display taxonomic predictions with improved analytical methods; and (4) effective ways to retrieve, search, and summarize results by integrating the predictions into the NCBI tree-based taxonomic information. GSTaxClassifier takes input nucleotide sequences and using a modified Bayesian model evaluates the genomic signatures between metagenomic query sequences and reference genome databases. The simulation studies of a numerical data sets showed that GSTaxClassifier could serve as a useful program for metagenomics studies, which is freely available at http://helix2.biotech.ufl.edu:26878/metagenomics/.
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Keywords
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Genomic signature; meta-genomics; taxonomy; Bayesian method
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Citation
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Yu et al., Bioinformation 4(1): 46-49 (2009) | |
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Edited by
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P. Kangueane
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ISSN
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0973-2063
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Publisher
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Biomedical Informatics
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License
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This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
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