PromoterWise (EBI)

PromoterWise (EBI) analyzes DNA sequences to detect conserved transcriptional motifs within promoter and transcription control regions while accommodating structural variations such as inversions and translocations.

Key Features:

• Specific Alignment Tool: Specialized alignment tailored to transcription control regions that accommodates inversions and translocations to preserve functional promoter elements.
• Motif Enumeration and Analysis: Exhaustive enumeration of all possible 12-mers with comparative analysis across mammals and vertebrates to identify conserved active transcriptional motifs.
• Experimental Validation: Incorporates experimental validation of predicted motifs, as demonstrated by studies in Medaka fish.

Scientific Applications:

• Cross-species motif identification: Identify conserved transcriptional motifs across mammalian and vertebrate genomes.
• Promoter and regulatory region analysis: Investigate the impact of structural rearrangements such as inversions and translocations on promoter function and gene regulation.
• Validation of computational predictions: Provide candidate motifs for experimental validation workflows, including studies in Medaka fish.

Methodology:

Sequence alignment tailored to transcription control regions, exhaustive enumeration of 12-mers, and comparative genomics across mammals/vertebrates to identify conserved motifs.