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The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

S. Luehr, H. Hartmann, J. Soding
2012 Nucleic Acids Research  
The XXmotif server provides (i) a list of significantly overrepresented motif PWMs with web logos and E-values; (ii) a graph with color-coded boxes indicating the positions of selected motifs in the input  ...  The discovery of regulatory motifs enriched in sets of DNA or RNA sequences is fundamental to the analysis of a great variety of functional genomics experiments.  ...  The most popular one is the MEME Suite server (5) , within which the position weight matrix (PWM)-based MEME and GLAM2 motif discovery programs can be run (6, 7) , alongside several related tools to  ... 
doi:10.1093/nar/gks602 pmid:22693218 pmcid:PMC3394272 fatcat:4yzo2nrp25b75b3kwr2rtl3dtq

SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences

Federico Agostini, Davide Cirillo, Riccardo Ponti, Gian Tartaglia
2014 BMC Genomics  
Results: Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment) algorithm for discovery of regulatory regions in nucleic acid sequences.  ...  SeAMotE provides (i) a robust analysis of high-throughput sequence sets, (ii) a motif search based on pattern occurrences and (iii) an easy-to-use web-server interface.  ...  Acknowledgements The authors would like to thank Roderic Guigó (CRG), Guillaume Filion (CRG), Andreas Zanzoni (Inserm, U1090), Giovanni Bussotti (EMBL-EBI) and Samuel Francis Reid (CRG) for stimulating  ... 
doi:10.1186/1471-2164-15-925 pmid:25341390 pmcid:PMC4223730 fatcat:ywfaywlgmjfgfjhpu3hyivbufi

MODSIDE: a motif discovery pipeline and similarity detector

Ngoc Tam L. Tran, Chun-Hsi Huang
2018 BMC Genomics  
The results include the common significant motifs from multiple tools, the motifs detected by some tools but not by others, and the best matches for each motif in the motif collection of multiple tools  ...  Results: Here we present MODSIDE, a motif discovery pipeline and similarity detector. The pipeline integrated four de novo motif finders: ChIPMunk, MEME, Weeder, and XXmotif.  ...  Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s12864-018-5148-1 fatcat:suy5zb4imzexpjhozul5zquhva

MCAT: Motif Combining and Association Tool

Yanshen Yang, Jeffrey A. Robertson, Zhen Guo, Jake Martinez, Christy Coghlan, Lenwood S. Heath
2019 Journal of Computational Biology  
Results: I present a novel and fast tool MCAT (Motif Combining and Association Tool) for de novo motif discovery by combining six state-of-the-art motif discovery tools (MEME, BioProspector, DECOD, XXmotif  ...  I present a novel and fast tool MCAT (Motif Combining and Association Tool) for motif discovery by combining six state-of-the-art motif discovery tools (MEME, BioProspector, DECOD, XXmotif, Weeder, and  ...  XXmotif (eXhaustive, weight matriX-based motif discovery) [29] is a weight matriX-based motif finding web server that has three stages: masking stage, pattern stage, and position weight matrices (PWM  ... 
doi:10.1089/cmb.2018.0113 pmid:30418034 fatcat:xwr4ptepyvdhvmih7pme2xdci4

DRIMust: a web server for discovering rank imbalanced motifs using suffix trees

Limor Leibovich, Inbal Paz, Zohar Yakhini, Yael Mandel-Gutfreund
2013 Nucleic Acids Research  
We present a new web application, named DRIMust, freely accessible through the website http://drimust. technion.ac.il for de novo motif discovery services.  ...  The DRIMust algorithm is based on the minimum hypergeometric statistical framework and uses suffix trees for an efficient enumeration of motif candidates.  ...  ACKNOWLEDGEMENTS The authors thank DRIMust's many users for their useful comments and suggestions for improving the website.  ... 
doi:10.1093/nar/gkt407 pmid:23685432 pmcid:PMC3692051 fatcat:27itw2tb2nfwrazlbwu5eqo4ba

P-value-based regulatory motif discovery using positional weight matrices

H. Hartmann, E. W. Guthohrlein, M. Siebert, S. Luehr, J. Soding
2012 Genome Research  
Here we present XXmotif (eXhaustive evaluation of matriX motifs), the first PWM-based motif discovery method that can optimize PWMs by directly minimizing their P-values of enrichment.  ...  For a given PWM, the enrichment P-value is calculated efficiently from the match P-values of all possible motif placements in the input sequences using order statistics.  ...  Acknowledgments We thank Mark Schroeder for providing us with the set of segmentation modules, insightful discussions, and for testing XXmotif.  ... 
doi:10.1101/gr.139881.112 pmid:22990209 pmcid:PMC3530678 fatcat:nqh45pooybghpecf4sp2vfdpc4

On the source-identification method

William M. Hartmann, Brad Rakerd, Joseph B. Gaalaas
1998 Journal of the Acoustical Society of America  
Acknowledgments We thank Mark Schroeder for providing us with the set of segmentation modules, insightful discussions, and for testing XXmotif.  ...  Many thanks to Claudia Gugenmus for testing initial versions of XXmotif and Anja Kiesel and Mark Heron for help with the human core promoter analysis.  ...  Here we present XXmotif (eXhaustive evaluation of matriX motifs), the first PWM-based motif discovery method that can optimize PWMs by directly minimizing their P-values of enrichment.  ... 
doi:10.1121/1.423936 pmid:9857513 fatcat:ovyks4s2rrg5dffkxl7ktpck2y