We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. After optimization, MAMA accurately simulated more than 87% of gene expression.
See Kakei Y, Ogo Y, Itai RN, et al. (2013) Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient. Rice 6(1): 22.

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Bio-Informatics

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Creative Commons Attribution Non-Commercial License V2.0

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Additional Project Details

Operating Systems

Windows

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Python, Perl, C

Related Categories

Python Bio-Informatics Software, Perl Bio-Informatics Software, C Bio-Informatics Software

Registered

2016-09-28