MOTIFSIM: A web tool for detecting similarity in multiple DNA motif datasets

• Published in: BioTechniques Vol. 59; no. 1; pp. 26 - 33
• Main Authors: Tran, Ngoc Tam L, Huang, Chun-Hsi
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis Group 01-07-2015
• Subjects: Algorithms; Datasets as Topic; DNA motif; Internet; motif detection tool; motif similarity; Nucleotide Motifs; p300-CBP Transcription Factors - chemistry; RNA Polymerase II - chemistry; Software; transcription factor binding site; User-Computer Interface; transcription factor binding site; DNA motif; motif detection tool; motif similarity
• ISSN: 0736-6205; 1940-9818
• DOI: 10.2144/000114308

Currently, there are a number of motif detection tools available that possess unique functionality. These tools often report different motifs, and therefore use of multiple tools is generally advised since common motifs reported by multiple tools are more likely to be biologically significant. However, results produced by these different tools need to be compared and existing similarity detection tools only allow comparison between two data sets. Here, we describe a motif similarity detection tool (MOTIFSIM) possessing a web-based, user-friendly interface that is capable of detecting similarity from multiple DNA motif data sets concurrently. Results can either be viewed online or downloaded. Users may also download and run MOTIFSIM as a command-line tool in stand-alone mode. The web tool, along with its command-line version, user manuals, and source codes, are freely available at http://biogrid-head.engr.uconn.edu/motifsim/.