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Motif Tool Assessment Platform (MTAP) MediaWiki
Automated regulatory motif detection is a fundamental problem in molecular biology. Currently, there are more than 140 different tools for identification of cis-regulatory motifs. Consequently, it is extremely difficult for the molecular biologist to know which tools are effective even on the most simple of genomes. A root cause of this is a lack of good datasets for benchmarking. The Motif Tool Assessment Platform (MTAP) is a resource for the scientific community with 2 goals: (1) provide an open source benchmarking platform for researchers in de novo motif detection and complementary evaluation datasets for benchmarking and (2) to provide benchmarks to assist the molecular biology community in determining the best tools to use in their domain of interest. Anyone in the community is allowed to edit this wiki, so that we can have the most correct and up to date information.
ToolPage
The Tool Page contains a listing of all of the de novo motif assessment tools we are aware of. If a tool is open source, we will write a parser for the tool and integrate it into our assessment platform and provide benchmarks for the community. References
Reviews
Need a place to get started? Here we provide a list of reviews and assessments of regulatory module discovery Reviews.
Assessments
As assessments are completed, we will make them available here.
Software
We have our first official release. Here it is: mtap.tar.gz
Publications
You may view our PSB 2007 poster here: Image:MyPoster.pdf
You may view our CSB 2009 poster here: Image:CSB2009.pdf
Support
MTAP is a joint project between the Department of Pathology and Microbiology at the University of Nebraska Medical Center and the College of Information Science and Technology at the University of Nebraska Omaha. MTAP is housed at the Peter Kiewit Institute on the University of Nebraska at Omaha. This research project was made possible by the NSF grant number EPS-0091900 and the NIH grant number P20 RR16469 from the INBRE Program of the National Center for Research Resources.
Contact Information
This project is headed by Daniel J Quest at the University of Nebraska Medical Center. Any questions about our assessments or requests for additional assessments can be directed to djquest at unmc dot edu. I will respond to you as quickly as possible. Any questions about software should be directed to Mohammad Shafiullah: mshafiullah.ne at gmail.com.
