C16S - a Hidden Markov Model based algorithm for taxonomic classification of 16S rRNA gene sequences.
Recent advances in high throughput sequencing technologies and concurrent refinements in 16S rDNA isolation techniques have facilitated the rapid extraction and sequencing of 16S rDNA content of microbial communities. The taxonomic affiliation of these 16S rDNA fragments is subsequently obtained using either BLAST-based or word frequency based approaches. However, the classification accuracy of such methods is observed to be limited in typical metagenomic scenarios, wherein a majority of organisms are hitherto unknown. In this study, we present a 16S rDNA classification algorithm, called C16S, that uses genus-specific Hidden Markov Models for taxonomic classification of 16S rDNA sequences. Results obtained using C16S have been compared with the widely used RDP classifier. The performance of C16S algorithm was observed to be consistently higher than the RDP classifier. In some scenarios, this increase in accuracy is as high as 34%. A web-server for the C16S algorithm is available at http://metagenomics.atc.tcs.com/C16S/.
Bio-sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, 1 Software Units Layout, Madhapur, Hyderabad, 500081, Andhra Pradesh, India. tarini@atc.tcs.com
Tarini Shankar
TS
Ghosh
Purnachander
P
Gajjalla
Monzoorul Haque
MH
Mohammed
Sharmila S
SS
Mande
D000465:Algorithms; D053938:DNA Fragmentation; D030541:Databases, Genetic; D008390:Markov Chains; D056186:Metagenomics; D008954:Models, Biological; D020560:Proteobacteria / Q000145:classification / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000145:classification* / Q000235:genetics*; D015203:Reproducibility of Results; D012231:Rhizobium / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods
D012336:RNA, Ribosomal, 16S