Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment.

ABSTRACT: 16S rRNA gene profiling has recently been boosted by the development of pyrosequencing methods. A common analysis is to group pyrosequences into Operational Taxonomic Units (OTUs), such that reads in an OTU are likely sampled from the same species. However, species diversity estimated from error-prone 16S rRNA pyrosequences may be inflated because the reads sampled from the same 16S rRNA gene may appear different, and current OTU inference approaches typically involve time-consuming pairwise/multiple distance calculation and clustering. I propose a novel approach AbundantOTU based on a Consensus Alignment (CA) algorithm, which infers consensus sequences, each representing an OTU, taking advantage of the sequence redundancy for abundant species. Pyrosequencing reads can then be recruited to

SUBMITTER: Ye Y 

PROVIDER: S-EPMC3217275 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature