Author(s)

Yi-Bo Wu, Li-Rong Yan, Hui Liu, Han-Chang Sun, Hong-Wei Xie

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Revealing biodiversity in microbial communities is essential in metagenomics researches. With thousands of sequenced 16S rRNA gene available, and advancements in oligonucleotide microarray technology, the detection of microor-ganisms in microbial communities consisting of hundreds of species may be possible. Many of the existing strategies developed for oligonucleotide probe design are dependent on the result of global multiple sequences alignment, which is a time-consuming task. We present a novel program named OligoSampling that uses MCMC method to design group-specific oli-gonucleotide probes. The probes generated by OligoSampling are group specific with weak crosshybridization potentials. Furthermore a high coverage of target sequences can be obtained. Our method does not need to globally align target sequences. Locally aligning target sequences iteratively based on a Gibbs sampling strategy has the same effect as globally aligning sequences in the process of seeking group-specific probes. OligoSampling provides more flexibility and speed than other software programs based on global multiple sequences alignment.

16S Rrna; Probe Design; MCMC

Wu, Y. , Yan, L. , Liu, H. , Sun, H. and Xie, H. (2009) A MCMC strategy for group-specific 16S rRNA probe design. Journal of Biomedical Science and Engineering, 2, 412-418. doi: 10.4236/jbise.2009.26059.