Precise

Precise predicts regulatory cis-acting elements within DNA sequences upstream of coding regions to identify conserved promoter motifs that mediate transcription factor binding and transcriptional regulation.

Key Features:

• Empirical Motif Frequency Tables: Utilizes empirical motif frequency tables generated from whole-genome sequences or other comprehensive datasets to filter and prioritize regulatory motifs.
• Motif Table Generation Tools: Includes analytical tools to create empirical motif frequency tables from genomic sequence data for downstream motif analysis.

Scientific Applications:

• Arabidopsis starch metabolism analysis: Built an empirical motif frequency table from upstream regions of all Arabidopsis genes and screened 64 upstream sequences from starch metabolism genes, identifying 20 high-specificity motifs, 15 of which showed homology to cis-acting elements regulated by light, auxin, and abscisic acid.
• Gibberellin induction analysis: Analyzed upstream regions of 16 gibberellin (GA)-induced Arabidopsis genes and recovered six of 17 known GA motifs when compared to the PLACE database.

Methodology:

Generates empirical motif frequency tables from genomic sequences, performs motif analysis on upstream promoter regions, and compares candidate motifs to the PLACE database.