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Table 1 Software programs used in Promzea

From: Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas

Tool

Description and download site

MEME

Multiple EM (Expectation Maximixation) for Motif Elicitation is a probabilistic de novo motif finding algorithm. It divides sequences into substrings and calculates the probability of each substring being a motif compared to the background. Each motif probability is recalculated during re-running using an expectation-maximisation algorithm. (http://meme.nbcr.net/downloads/meme_4.6.0.tar.gz)

Bioprospector

Gibbs sampling algorithm. Motif width is user-defined. The sequences are randomly searched to find similar motifs. Newly discovered PWM motifs are scored relative to the background. The operation is repeated until conversion of the results. Results are different at each run. (http://motif.stanford.edu/distributions/bioprospector)

Weeder

Consensus enumeration program; finds similar consensus sequences in data allowing 1 to 3 mismatches. The search is extended to the adjacent bases of the word to define the final motif. (http://159.149.160.51/modtools)

PSCAN

Determines the probability that a defined PWM motif exists in each database sequence relative to its best score. (http://159.149.160.51/pscan/)

FIMO

Finds occurrence of each defined PWM in a sequence database using a p-value calculation relative to the Markov background. (http://meme.nbcr.net/downloads/meme_4.6.0.tar.gz)

Clover

Finds occurrence of each defined PWM in a sequence database using PWM best scores compared to the background. (http://zlab.bu.edu/clover)