Promzea is a Perl-based application to discover de novo motifs underlying co-regulated genes in maize, Arabidopsis or rice.

Users can enter cDNA (full length or partial) sequences, gene IDs or Affymetrix microarray probe IDs (maize). Corresponding upstream or first-intron sequences (maize) are retrieved from the plant genome (inbred B73, Col-0, Oryza sativa japonica) as shown below in Figure 1. Promzea searches the retrieved sequences using three motif discovery tools (Weeder, Bioprospector and MEME). Predicted motifs are filtered, combined and ranked and then displayed for the user along with a ranking score (MNCP see publication). Finally, Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the complete gene list and corresponding gene annotations, along with other forms of validation for the user to analyze the results

This software incorporates the following proprietary software: Weeder, MEME, BioProspector, FIMO, Pscan and Clover. Users are encouraged to cite both Promzea and all original references pertaining to these included software programs. Use of Promzea is restricted to the academic and non-profit research community. It is the responsibility of any for-profit corporation who wishes to use Promzea to gain permission from the developers of Weeder, MEME, FIMO, BioProspector, Pscan, and Clover.

Promzea was developed by Christophe Liseron-Monfils in the lab of Manish Raizada at the University of Guelph, Canada.

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