The Block Gibbs Sampler for RNA Prediction (RNAG)

The Block Gibbs Sampler for RNA Prediction (RNAG)

The Block Gibbs Sampler for RNA Prediction (RNAG)

RNAG is temporarily out of service. We hope to be back online soon. We aplogize for the inconvenience.

RNAG is an application for the prediction of the RNA secondary structure common to multiple unaligned sequences (Wei et.al. Bioinformatics,27:2486-2493 2011). It uses a blocked Gibbs Sampler strategy that has has a theoretical advantage in convergence time (Liu, J Amer. Stat. Assoc,89:958, 1994). This Bayesian sampling algorithm returns structural predictions using gamma centroid estimators (Hamada, et.al. Bioinformatics, 25:465, 2009), which allow the user to adjust the sensitivity specificity trade off. Sampled structures provide for a more complete characterization of posterior space in two ways: a clustering of sampled structures for the evidence of mufti-modality of the posterior space, and assessment of the uncertainty of predictions using Bayesian confidence limits (Webb-Robertson, PloS Comp Bio, doi:10.1371/journal.pcbi.1000077, 2008).



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