MoD Tools

MoD Tools detects conserved sequence and secondary-structure motifs in nucleotide and RNA sequences to identify regulatory elements involved in transcriptional and post-transcriptional gene regulation.

Key Features:

• Weeder: Identifies conserved transcription factor binding sites (TFBSs) within nucleotide sequences from co-regulated genes.
• WeederH: Extends Weeder to detect TFBSs and distal regulatory modules within sequences from homologous genes.
• RNAProfile: Discovers conserved secondary-structure motifs in unaligned RNA sequences of RNAs with unknown secondary structure.

Scientific Applications:

• Co-regulated gene analysis: Compare co-regulated genes to identify conserved regulatory motifs that may coordinate transcriptional control.
• Comparative genomics of homologs: Analyze homologous genes across species to uncover evolutionary conserved TFBSs and distal regulatory modules.
• Post-transcriptional regulation: Investigate mRNA and other RNA sequences to discover conserved secondary-structure motifs that may affect RNA stability or translation.

Methodology:

MoD Tools applies a combination of computational algorithms to detect conserved sequence motifs and conserved RNA secondary-structure motifs in nucleotide and unaligned RNA sequences.