Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap

By Gavin A. Price, Gavin E. Crooks, R. Green, Steven E. Brenner. 2005

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Hidden Markov model speed heuristic and iterative HMM search procedure (2010, methodology): “In order to assess the significance of the performance differences between algorithms on our benchmark, we have utilized a bootstrapping approach [15].”
Accelerated Profile HMM Searches (2011, neutral): “Empirically too, any danger has seemed negligible, because profmark benchmarks tend to be broadly concordant with other published benchmarks [28,44].”
NetB, a New Toxin That Is Associated with Avian Necrotic Enteritis Caused by Clostridium perfringens (2008, methodology): “These unique ORFs were further analysed by PSORTB [19] and ProteomeAnalyst [20] to identify predicted extracellular proteins.”
A Binary Classification Framework for Two-Stage Multiple Kernel Learning (2012, methodology): “The first two datasets are for the problem of bacterial protein locations (Gardy et al., 2004).”
A benchmark of multiple sequence alignment programs upon structural RNAs (2005, background): “Dynalign second edition [17,18] Simultaneously aligns and predicts the lowest free energy RNA secondary structure common to two sequences.”