TargetRNA

TargetRNA predicts mRNA targets of bacterial small non-coding RNAs (sRNAs) by identifying potential base-pairing interactions within annotated bacterial genomes.

Key Features:

• Dynamic programming algorithm: Uses a dynamic programming algorithm to search for base-pairing interactions between an input sRNA sequence and annotated mRNAs.
• Genome-wide mRNA screening: Evaluates each annotated mRNA in a specified bacterial genome for binding compatibility with the input sRNA sequence.
• Ranked candidate targets: Generates a ranked list of candidate mRNA targets based on predicted basepairing interaction potential.
• Experimental validation: Predictions have been substantiated through experimental validations across multiple bacterial organisms.

Scientific Applications:

• Target prioritization: Prioritizes candidate mRNAs for experimental validation and downstream functional studies.
• Posttranscriptional regulation analysis: Enables analysis of sRNA-mediated posttranscriptional regulation in bacterial gene expression.
• Microbial genomics and molecular biology: Supports studies that require identification of sRNA–mRNA interactions in bacterial systems.

Methodology:

A dynamic programming algorithm searches annotated mRNAs in a specified bacterial genome for potential basepair-binding interactions with an input sRNA sequence and ranks mRNAs by predicted basepairing interaction potential.