PatSearch

PatSearch identifies complex patterns within genomic sequences to detect oligonucleotide consensus sequences, RNA secondary-structure elements (including iron responsive element hairpin-loops), and motifs modelled by position-weight matrices for genome-wide regulatory analysis.

Key Features:

• Pattern Matching Capabilities: Searches for intricate combinations of oligonucleotide consensus sequences to identify cis-acting elements that interact with trans-acting protein factors for genome annotation and comparative analyses.
• Secondary Structure Detection: Identifies RNA secondary structure elements, including the iron responsive element hairpin-loop structure, relevant to post-transcriptional regulation.
• Position-Weight Matrices (PWMs): Utilizes PWMs to model sequence motifs with varying degrees of conservation, enabling flexible and precise motif detection across genomic datasets.
• Mismatch Tolerance: Allows a user-defined threshold for mismatches or mispairings to detect biologically relevant but non-perfectly conserved patterns.

Scientific Applications:

• Iron Homeostasis Analysis: Detection of iron responsive element hairpin-loop structures to study regulatory mechanisms of iron metabolism.
• p53 Regulatory Element Identification: Locating p53 responsive elements to investigate cell cycle regulation and tumor suppression pathways.
• Promoter Module Analysis: Detecting promoter modules containing CAAT-, TATA-, and cap-boxes to analyze transcription initiation and gene regulatory networks.

Methodology:

PatSearch employs a flexible and fast algorithm that integrates multiple pattern matching criteria, enabling comprehensive searches across large genomic datasets, and supports a user-defined mismatch threshold for tailored sensitivity.