T-Coffee API (EBI)

T-Coffee API (EBI) performs multiple sequence alignment by integrating local and global pairwise alignments into a consistency-based library to improve alignment accuracy for phylogenetic, structural, and comparative genomic analyses.

Key Features:

• Hybrid Alignment Approach: Combines local and global pairwise alignments to construct a comprehensive library of alignment information that informs downstream alignment steps.
• Integration of Heterogeneous Data Sources: Incorporates outputs from diverse alignment programs and structural superpositions to enrich the alignment library.
• Progressive Alignment Enhancement: Uses a pre-processed dataset containing all pairwise alignments among sequences to guide progressive alignment and consider broader inter-sequence relationships.
• Empirical Validation and Performance: Demonstrated improved alignment accuracy in benchmark testing across 141 diverse test cases, particularly for sequences with wide phylogenetic distributions.

Scientific Applications:

• Phylogenetic Analysis: Produces alignments that support inference of evolutionary relationships among sequences across wide phylogenetic distances.
• Structural Biology: Assists alignment of protein sequences and integration with structural superpositions from experimental or computational models.
• Comparative Genomics: Facilitates comparison of genomic sequences across species to identify conserved elements and functional domains.

Methodology:

Combines local and global pairwise alignments, constructs a library of all pairwise alignments (including outputs from other alignment programs and structural superpositions), and applies a consistency-based progressive alignment guided by that library.