T-Coffee (SIB)

T-Coffee (SIB) computes consistency-based multiple sequence alignments of DNA, RNA, and protein sequences and their structures for comparative, evolutionary, and structural analyses.

Key Features:

• T-Coffee mode: Default consistency-based alignment for protein and nucleic acid sequences.
• M-Coffee mode: Integrates outputs from multiple aligners into a consensus to improve overall alignment quality.
• Expresso (template-based): Aligns proteins using known 3D structural templates to increase alignment accuracy.
• R-Coffee (template-based): Aligns RNA sequences using conserved secondary structure information to improve precision.
• PSI-Coffee (template-based): Employs homology extension to achieve accurate alignments of distantly related sequences.
• Consistency-based algorithm: Integrates multiple sources of sequence similarity by combining direct pairwise comparisons and indirect information from other alignments.
• Scalability: Improved algorithmic implementation to handle datasets up to 150 sequences with lengths reaching 10,000 residues.

Scientific Applications:

• Structural biology: Aligns protein 3D structures and RNA secondary structures to support interpretation of molecular function and interactions.
• Evolutionary studies: Aligns distantly related sequences to support phylogenetic inference and homology analyses.
• Comparative genomics: Provides precise multiple sequence alignments for comparative analyses across genomes.

Methodology:

Uses a consistency-based approach that integrates multiple sources of sequence similarity, considering both direct pairwise comparisons and indirect information derived from other alignments, with algorithmic improvements to handle up to 150 sequences of lengths up to 10,000 residues.