SARA-Coffee

SARA-Coffee computes multiple RNA sequence alignments by integrating sequence and 3D structural information to improve alignment accuracy.

Key Features:

• Structure-Based Alignment: Leverages both nucleotide sequence and 3D structural information to align RNAs, accommodating sequences with or without known 3D structures.
• Integration of Pairwise and Multiple Aligners: Combines the SARA pairwise RNA structure aligner with the R-Coffee multiple alignment framework within the T-Coffee distribution to enhance alignment accuracy compared with sequence-only methods.
• Reliability Index: Reports a reliability index for each sequence, alignment column, and aligned residue to indicate confidence in alignment positions.

Scientific Applications:

• Structural Biology: Analysis of structural relationships and conserved 3D motifs among RNA molecules.
• Comparative Genomics: Comparative analysis of RNA sequences across species or within gene families incorporating structural information.
• Molecular Evolution: Investigation of evolutionary patterns and functional conservation of RNA structure.

Methodology:

Pairwise structural alignments are generated using SARA and these alignments are integrated into a multiple sequence alignment via R-Coffee within the T-Coffee framework.