AIModules

AIModules identifies transcription factor binding sites (TFBSs) and other nucleotide motifs in DNA and RNA and provides comparative evaluation to reduce TFBS overprediction.

Key Features:

• Matrix Utilization: Searches using predefined matrices from the JASPAR 2022 database or user-provided custom matrices.
• Multi-sequence Analysis: Identifies TFBSs common across multiple sequences to support comparative analyses.
• Conservation Filtering: Applies user-specified high or low conservation criteria to refine motif calls.
• Motif Scope: Detects diverse nucleotide motifs in DNA and RNA, including polyadenylation signals, enhancers, and silencers.
• Comparative Evaluation: Performs comparative evaluation of motif occurrences to address TFBS overprediction.
• Module Detection and Performance: Optimized for speed to enable detection of specific combinations of TFBSs (modules).

Scientific Applications:

• Promoter Analysis: Analyzes promoters to identify conserved modules and shared TFBSs within conserved gene families.
• Regulatory Element Detection: Detects regulatory motifs or modules in mRNA to support studies of post-transcriptional regulation.
• Comparative Genomics: Identifies conserved TFBSs and modules across sequences for comparative genomics investigations.

Methodology:

Performs matrix-based scanning using JASPAR 2022 or custom matrices, comparative evaluation across multiple sequences, application of high/low conservation thresholds, scanning for DNA and RNA motifs (including polyadenylation signals, enhancers, and silencers), and detection of TFBS combinations (modules).