GIMSAN: a Gibbs Motif Finder with Significance Analysis

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2008 Aug 16

PMID 18703586

Citations 20

Authors

Patrick Ng

Uri Keich

Affiliations

Soon will be listed here.

Abstract

Unlabelled: We present GIMSAN (GIbbsMarkov with Significance ANalysis): a novel tool for de novo motif finding. GIMSAN combines GibbsMarkov, our variant of the Gibbs Sampler, described here for the first time, with our recently introduced significance analysis.

Availability: GIMSAN is currently available as a web application and a stand-alone application on Unix and PBS (Portable Batch System) cluster through links from http://www.cs.cornell.edu/~keich.

Citing Articles

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Homer C, Summers D, Goranov A, Clarke S, Wiesner D, Diedrich J Cell Host Microbe. 2016; 19(6):849-64.

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PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

Danan C, Manickavel S, Hafner M Methods Mol Biol. 2015; 1358:153-73.

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Genome-wide replication landscape of Candida glabrata.

Descorps-Declere S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L BMC Biol. 2015; 13:69.

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Improving MEME via a two-tiered significance analysis.

Tanaka E, Bailey T, Keich U Bioinformatics. 2014; 30(14):1965-73.

PMID: 24665130 PMC: 4080741. DOI: 10.1093/bioinformatics/btu163.

GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

Liachko I, Youngblood R, Tsui K, Bubb K, Queitsch C, Raghuraman M PLoS Genet. 2014; 10(3):e1004169.

PMID: 24603708 PMC: 3945215. DOI: 10.1371/journal.pgen.1004169.