GENETIC ALGORITHMGIBBS SAMPLINGMOTIF DISCOVERYMotif discovery has been one of the most widely studied problems in bioinformatics ever since genomic and protein sequences have been available. In particular, (I,d)-motif discovery in nucleotide sequences has been, and still is, one of the most ...
GibbsSampling ••AlignACE:firststatisticalmotiffinderBioProspector:improvedversionofAlignACE Algorithm(sketch):1.Initialization:a.Selectrandomlocationsinsequencesx1,…,xNb.ComputeaninitialmodelMfromtheselocations 2.SamplingIterations:a.Removeonesequencexib.Recalculatemodelc.Pickanewlocationofmotifinxiaccordingto...
During the sampling process, PSFM is improved via a genetic algorithm. A post-processing with adaptive adding and removing is used to handle general cases with arbitrary numbers of instances per sequence. So Motif GibbsGA is capable of discovering several different motifs with differing numbers of...
4. Hybrid Gibbs-Sampling Algorithm for Challenging Motif Discovery: Gibbs DST [C] . Kazuhito Shid International Conference on Genome Informatics . 2006 机译:挑战基序的混合GIBBS - 采样算法:GIBBS DST 5. Uniqueness of Gibbs measures with application to Gibbs sampling and the Sum-Product algorith...
cluster analysis and motif finding for the analysis of microarray data. Starting from the expression, we present our adaptive quality-based clustering algorithm to define groups of tightly coexpressed genes. The upstream region is then retrieved based on the accession number and gene name. Once the...
Hybrid Gibbs-Sampling Algorithm for Challenging Motif Discovery: GibbsDST The difficulties of computational discovery of transcription factor binding sites (TFBS) are well represented by (l, d) planted motif challenge problems. L... K Shida - 《Genome Informatics》 被引量: 8发表: 2006年 加载更多...
The XDD motif is essential for catalytic activity and motif E contains the E(F/Y)XS site. Premotif A has a conserved lysine and two arginine residues (Kukkonen et al., 2005). The five major motifs for viral RNA polymerases were also present in OXBV. The coding regions of the full-...
This weighted Gibbs sampling method has been implemented andsuccessfully tested on both simulated and biological sequence data. Our experimental results demon-strate that the use of sequence weighting has a profound impact on the performance of a Gibbs motifsampling algorithm.~a...
Shida, K.: GibbsST: a Gibbs sampling method for motif discovery with enhanced resis- tance to local optima. BMC Bioinformatics 7 (2006)Shida K (2006) GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima. BMC Bioinformatics 7:486....
difference of our algorithm is that we make use of the trans- formed probability weight matrix tosample our data Sampling Algorithm for Challenging Motif Discovery: GibbsDST", GenomeInformatics, 17(2):3-13, 2006 [4] Shida K., "GibbsST: a Gibbs sampling method for motifJEA Pascual...