T-Reg Comparator

T-Reg Comparator compares position weight matrices (PWMs) and binding site sequences against the T-Reg database to identify motif similarities and support transcriptional regulation analysis.

Key Features:

• Motif comparison: Matches user-supplied PWMs or binding site sequences to entries in the T-Reg database and detects similarities including submatrix matches.
• Sequence scanning with weight matrices: Scans input sequences using PWMs to locate motif occurrences.
• Database integration: Utilizes the T-Reg database containing PWMs integrated from Transfac and Jaspar.
• Detailed reporting: Produces reports that summarize and highlight similarities between input motifs and database motifs.

Scientific Applications:

• Motif finding: Aids identification of transcription factor binding sites by comparing experimental motifs to known PWMs.
• Regulatory module discovery: Supports detection of related motifs that contribute to regulatory modules and gene regulatory network analysis.
• Annotation of regulatory genomic regions: Assists annotation of genomic regions with putative regulatory elements based on motif similarity.

Methodology:

Transcription factor binding sites are encoded as position weight matrices (PWMs), input PWMs or binding site sequences are compared against the T-Reg database (which integrates PWMs from Transfac and Jaspar), similarities including submatrix matches are detected, sequence scanning is performed using weight matrices, and detailed similarity reports are generated.