Match

Match identifies putative transcription factor binding sites (TFBS) in DNA sequences using weight matrix-based approaches and the matrix library from the TRANSFAC database.

Key Features:

• Integration with TRANSFAC Database: Uses TRANSFAC's comprehensive collection of weight matrices that represent transcription factor binding specificities.
• Optimized Search Modes: Implements sets of optimized matrix cut-off values to adjust search stringency and balance sensitivity versus specificity.
• User Profiles: Supports creation and reuse of profiles consisting of selected subsets of matrices with default or user-defined cut-off values.
• Tissue-Specific Profiles: Provides pre-compiled tissue-specific matrix profiles developed by the TRANSFAC team for targeted analyses.

Scientific Applications:

• Gene regulation analysis: Identification of candidate TFBS to study regulatory elements controlling gene expression.
• Transcription factor dynamics: Mapping potential binding sites to investigate transcription factor occupancy and activity patterns.
• Regulatory network elucidation: Supporting reconstruction of transcriptional regulatory networks by locating putative binding interactions.
• Interpretation of gene expression in health and disease: Providing candidate regulatory sites to explore mechanisms underlying expression changes associated with phenotypes or pathologies.

Methodology:

Searches DNA sequences with weight matrix-based scoring using TRANSFAC matrices and applies optimized matrix cut-off values to call matches from user-selected or tissue-specific subsets of matrices.