TFBSTools

TFBSTools provides functions to convert and analyze transcription factor binding site (TFBS) profile matrices and to scan genomic sequences and alignments for putative TFBSs to support studies of gene regulation.

Key Features:

• Matrix Conversion System: Converts between Position Frequency Matrix (PFM), Position Weight Matrix (PWM), and Information Content Matrix (ICM).
• Sequence Scanning: Scans sequences and alignments, including whole-genome datasets, to identify putative TFBSs.
• Database Querying: Queries the JASPAR database for transcription factor profiles.
• De Novo Motif Discovery: Provides a wrapper for de novo motif discovery software to identify novel motifs within datasets.
• Extensibility: Supports integration with statistical analyses, data visualization, and diverse datasets.

Scientific Applications:

• Identification of Regulatory Elements: Detects candidate regulatory elements by locating TFBSs from profile matrices and sequence scans.
• Transcription Factor Dynamics: Facilitates comparison of TF profiles and scanning results to study transcription factor binding behavior.
• Evolutionary Conservation: Enables analysis of conservation of binding sites across species using alignments.

Methodology:

Performs matrix conversions between PFM, PWM, and ICM; scans sequences and alignments for TFBSs; queries the JASPAR database for TF profiles; and wraps de novo motif discovery software.