Title |
INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences
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Published in |
BMC Genomics, November 2011
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DOI | 10.1186/1471-2164-12-s3-s4 |
Pubmed ID | |
Authors |
Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Rachamalla Maheedhar Reddy, Chennareddy Venkata Siva Kumar Reddy, Nitin Kumar Singh, Sharmila S Mande |
Abstract |
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. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Brazil | 2 | 3% |
Portugal | 1 | 1% |
United Kingdom | 1 | 1% |
New Zealand | 1 | 1% |
United States | 1 | 1% |
Unknown | 63 | 91% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 19 | 28% |
Researcher | 14 | 20% |
Student > Master | 11 | 16% |
Student > Bachelor | 6 | 9% |
Other | 4 | 6% |
Other | 8 | 12% |
Unknown | 7 | 10% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 35 | 51% |
Biochemistry, Genetics and Molecular Biology | 9 | 13% |
Computer Science | 8 | 12% |
Engineering | 2 | 3% |
Medicine and Dentistry | 2 | 3% |
Other | 2 | 3% |
Unknown | 11 | 16% |