T-Coffee (EBI)

T-Coffee (EBI) performs multiple sequence alignment by integrating local and global pairwise alignments and heterogeneous alignment sources into a library that guides progressive alignments to improve alignment accuracy.

Key Features:

• Library-based alignment: Pre-processing generates a library of pairwise alignments that informs the progressive alignment process.
• Integration of local and global alignments: The method leverages both local and global pairwise alignments to capture complementary alignment signals.
• Heterogeneous data sources: Alignment information can be derived from various alignment programs and structural superpositions to enrich the library.
• Performance validation: The approach was evaluated on 141 test cases and showed improved performance across datasets with varied phylogenetic spreads.

Scientific Applications:

• Comparative genomics: Producing accurate MSAs for genome-scale sequence comparisons and conserved region identification.
• Structural biology: Incorporating structural superpositions to improve alignments used in structure-function analyses.
• Phylogenetic analysis: Generating reliable alignments for sequences with significant evolutionary divergence to support phylogeny reconstruction.

Methodology:

Pre-processing builds a library of pairwise alignments from local and global pairwise methods and heterogeneous sources (various alignment programs and structural superpositions) that is used to guide a progressive alignment algorithm.