RNArobo

RNArobo searches for RNA structural motifs within long genomic sequences using both sequence and secondary-structure constraints to identify distant homologs of functional RNAs.

Key Features:

• Enhanced Descriptor Language: Builds upon the RNAbob descriptor language and supports specifying insertions within helices to represent complex secondary-structure elements.
• Efficient Algorithm Design: Employs an algorithm to address the NP-hard problem of RNA motif search by resolving the element ordering problem rather than relying on traditional backtracking.
• Speed Optimization: Achieves more than a 100-fold speedup in searching for complex motifs compared to previously published tools.
• Pseudoknot Handling: Includes a method to search complex motifs containing pseudoknots.

Scientific Applications:

• Identification of functional RNAs: Enables identification and analysis of ribozymes and aptamers within genomic sequences by combining sequence and secondary-structure constraints.
• Discovery of distant homologs: Facilitates finding distant homologs of known functional RNAs across long genomic sequences.

Methodology:

Addresses the element ordering problem and employs an algorithm to tackle the NP-hard RNA motif search problem, extends the RNAbob descriptor language to specify insertions within helices, and includes a method for searching motifs with pseudoknots.