jPREdictor

jPREdictor predicts genome-wide cis-regulatory elements by detecting clusters of short motifs (simple sequence motifs or position-specific scoring matrices, PSSMs) that bind regulatory proteins to elucidate gene regulatory control.

Key Features:

• Motif-Based Prediction: Detects clusters composed of individual motifs derived from simple sequence motifs or PSSMs.
• Multi-Motif Combinations: Combines individual motifs into multi-motifs with user-defined minimum and maximum distance constraints.
• Weighted Scoring System: Evaluates motif clusters using weights derived from positive and negative training sets to distinguish functional sites from non-functional sequences.
• Application Example: Has been applied to predict Polycomb/Trithorax Response Elements (PREs) in Drosophila melanogaster.

Scientific Applications:

• Gene regulation analysis: Enables genome-wide identification of cis-regulatory elements to study spatial and temporal modulation of gene expression.
• Developmental biology: Supports analysis of regulatory elements underlying developmental processes involving regulators such as Polycomb and Trithorax complexes.
• Evolutionary studies: Facilitates comparative analysis of regulatory networks across species to investigate evolutionary changes in gene regulation.

Methodology:

Detects individual motifs (simple motifs or PSSMs), identifies clusters of these motifs, assembles multi-motif combinations with specified distance constraints, and computes weighted scores using positive and negative training sets.