MelinaII

MelinaII predicts potential DNA motifs and transcription factor binding sites (TFBS) in promoter regions to support analyses of gene regulation and comparative genomics.

Key Features:

• Integration of multiple motif prediction algorithms: Integrates Consensus, MEME, Gibbs Sampler, MDScan, and Weeder for motif discovery.
• Simultaneous algorithm execution: Allows running up to four motif prediction algorithms concurrently for comparative analysis.
• Comparative analysis of predictions: Produces comparative outputs that enable assessment of motif predictions across different algorithms.
• Weight matrix construction and genome scanning: Constructs weight matrices (position weight matrices) from predicted motifs and applies them to upstream sequences across genomes including human, mouse, Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis, and Arabidopsis thaliana.
• Database comparison: Applies constructed weight matrices to public motif databases such as JASPAR and DBTBS to identify similar motifs.

Scientific Applications:

• Promoter motif discovery: Identification of potential DNA motifs and TFBS within promoter regions to inform studies of transcriptional regulation.
• Comparative genomics: Cross-genome scanning of motifs in human, mouse, Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis, and Arabidopsis thaliana for comparative and evolutionary analyses.
• Motif annotation: Matching predicted motifs to entries in JASPAR and DBTBS to annotate and identify conserved regulatory elements.

Methodology:

Integrates Consensus, MEME, Gibbs Sampler, MDScan, and Weeder; supports concurrent execution of up to four algorithms; constructs weight matrices from predicted motifs; scans upstream sequences across specified genomes; and compares matrices to JASPAR and DBTBS, producing comparative outputs.