SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

Area of Science:

• Bioinformatics
• Computational Biology
• Structural Biology

Background:

• Accurate multiple RNA sequence alignment is crucial for understanding RNA structure and function.
• Existing methods often struggle to integrate structural information effectively.
• Combining sequences with and without known 3D structures presents a significant challenge.

Purpose of the Study:

• To introduce the SARA-Coffee web server for 3D structure-based multiple RNA sequence alignment.
• To provide a reliable tool for aligning RNA sequences, incorporating both structural and sequence data.
• To enhance the accuracy of multiple RNA sequence alignments by leveraging structural information.

Main Methods:

• Development of the SARA-Coffee web server.
• Integration of SARA (pairwise structural RNA aligner) with R-Coffee (multiple RNA aligner).
• Computation of 3D structure-based multiple RNA sequence alignments.

Main Results:

• SARA-Coffee enables the online computation of multiple RNA sequence alignments.
• The server successfully combines RNA sequences with and without known 3D structures.
• Reliability indices are provided for each sequence, column, and aligned residue.
• Improved alignment accuracy compared to most sequence-only aligners when structural data is available.

Conclusions:

• SARA-Coffee offers an effective approach for structure-based multiple RNA sequence alignment.
• The web server provides valuable reliability metrics for alignment assessment.
• This tool has the potential to advance research in RNA structure, function, and evolution.