MARNA web server

MARNA web server performs multiple sequence-structure alignments of RNA molecules to integrate primary sequence and secondary structure information for accurate comparative analysis of RNA families.

Key Features:

• Pairwise Sequence-Structure Alignment: Performs pairwise alignments that evaluate both nucleotide sequences and RNA secondary structures.
• Multiple Alignment Integration: Integrates multiple RNA alignments by generating libraries of weighted alignment edges from pairwise comparisons reflecting sequence conservation and structural integrity.
• Handling Missing Structural Information: Generates secondary-structure information for sequences lacking explicit structure by sampling low-energy conformations.
• Utilization of T-Coffee System: Processes generated libraries using the T-Coffee consistency-based multiple alignment system.
• Consensus Extraction: Extracts consensus sequences and consensus secondary structures from the multiple alignments.

Scientific Applications:

• RNA family comparative analysis: Aligns RNAs where both primary sequence and secondary structure are critical for function to identify conserved motifs.
• Analysis with incomplete structural data: Enables analysis of datasets containing sequences without known secondary structures by sampling low-energy conformations.
• Benchmarking on Rfam datasets: Has been applied to datasets from the Rfam database to evaluate alignment performance on curated RNA families.

Methodology:

Conducting pairwise sequence-structure alignments; generating libraries of weighted alignment edges from pairwise comparisons; sampling low-energy conformations to supply missing secondary-structure information; processing the libraries with the T-Coffee system to produce a consistent multiple alignment; and extracting consensus sequences and structures from the aligned data.