MTAP: The Motif Tool Assessment Platform

Background: In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with the best performance characteristics for specific problem domains. Identifying the correct tool is difficult because of the great variability in motif detection software. Consequently, many labs spend considerable effort testing methods to find one that works well in their problem of interest. Results: In this work, we propose a method (MTAP) that substantially reduces the effort required to assess de novo regulatory motif discovery software. MTAP differs from previous attempts at regulatory motif assessment in that it automates motif discovery tool pipelines (something that traditionally required many manual steps), automatically constructs orthologous upstream sequenc...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham H. Ali
• Keywords: BMCBI 2008, Regulatory Motif Assessment, Regulatory Motif Discovery, Tools