The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multiple transcription factors simultaneously in unaligned DNA sequences that may be...

We introduce a methodology for performing approximate computations in very complex probabilistic systems (e.g. huge pedigrees). Our approach, called blocking Gibbs, combines exact local computations with Gibbs sampling in a way that complements the strengths of both. The methodology is illustrated on a real-world problem involving a heavily inbred pedigree containing 20;000 individuals. We pres...

We consider various versions of adaptive Gibbs and Metropoliswithin-Gibbs samplers, which update their selection probabilities (and perhaps also their proposal distributions) on the fly during a run, by learning as they go in an attempt to optimise the algorithm. We present a cautionary example of how even a simple-seeming adaptive Gibbs sampler may fail to converge. We then present various pos...