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User Documentation

Installing PRIORITY

Download the zip file and unzip it to the location of your choice.


On Mac OS X, simply double click the PRIORITY application bundle. On all other operating systems, run priority.jar, either by double clicking it or by opening up a command prompt or shell and typing:

java -jar priority.jar

Explanations for all the fields and descriptions of all the available parameters are provided in the PRIORITY README file, which can also be accessed from within the program by visiting the Help menu.

Research Papers

The primary publication describing the PRIORITY algorithm, along with results and comparisons to state-of-the-art motif finding algorithms, is:

  1. Narlikar, L., Gordân, R., Ohler, U., & Hartemink, A. (2006) “Informative priors based on transcription factor structural class improve de novo motif discovery.” Intelligent Systems in Molecular Biology 2006 (ISMB06), Bioinformatics, 22, July 2006. pp. e384–e392.

The class priors used by PRIORITY were derived from three classifiers built as described in:

  1. Narlikar, L. & Hartemink, A. (2006) “Sequence Features of DNA Binding Sites Reveal Structural Class of Associated Transcription Factor.” Bioinformatics, 22, January 2006. pp. 157–163.

The classifiers were trained using the SMLR algorithm, which is described in:

  1. Krishnapuram, B., Figueiredo, M., Carin, L., & Hartemink, A. (2005) “Sparse Multinomial Logistic Regression: Fast Algorithms and Generalization Bounds.” IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 27, June 2005. pp. 957–968.