PMSearch

PMSearch predicts putative transcription factor binding sites (TFBSs) in DNA sequences using Position Frequency Matrices (PFMs) to support promoter prediction and transcriptional regulation studies.

Key Features:

• Input Flexibility: Accepts user-defined PFMs or a local dataset of 507 PFMs sourced from Transfac Public 7.0 and JASPAR.
• Comprehensive Scanning: Scans DNA sequences with provided PFMs and scores matches to identify high-scoring candidate TFBSs.
• Detailed Output Presentation: Provides a plot of predicted TFBS distribution along the DNA sequence, a table listing each putative binding site with location, score, and associated motif, and clusters of predicted binding sites highlighting regions with multiple potential interactions.
• Enhanced Analysis Tools: Links predicted motifs to clusters of PFMs similar to the input matrices to support comparative motif analysis.

Scientific Applications:

• Transcriptional regulation studies: Identification of putative TFBSs to analyze regulatory control of gene expression.
• Promoter prediction: Localization of candidate regulatory elements within promoter regions using motif scanning with PFMs.
• Motif clustering and comparative analysis: Exploration of related PFMs and clustered binding sites to detect motif families and combined regulatory regions, facilitating identification of potential targets for genetic or pharmaceutical intervention.

Methodology:

Uses Position Frequency Matrices (PFMs) to scan and score DNA sequences for TFBS prediction and accepts user-defined PFMs or a local set of 507 PFMs from Transfac Public 7.0 and JASPAR.