Abalign

Abalign performs ultrafast multiple-sequence alignment and immunoglobulin-specific processing of high-throughput B-cell receptor (BCR) and antibody sequencing data to enable repertoire-level analysis for studies of adaptive immunity and antibody development.

Key Features:

• Ultrafast Multiple Sequence Alignment (MSA): Performs ultrafast MSA of BCR/antibody sequences with comparable or superior accuracy to state-of-the-art MSA tools while reducing time and memory consumption.
• Immunoglobulin-specific information: Provides detailed immunoglobulin-specific annotations essential for BCR analysis.
• BCR extraction: Extracts B-cell receptors from high-throughput sequencing (HTS) data.
• VJ gene assignment: Assigns V and J genes to BCR sequences accurately.
• Clonotype analysis: Analyzes clonotypes to characterize immune response patterns.
• Mutation profiling: Profiles mutations within BCR sequences to identify somatic hypermutations.
• Lineage tree construction: Constructs lineage trees to represent evolutionary relationships among BCR sequences.
• Repertoire comparison: Compares BCR immune repertoires across samples or experimental conditions.
• Scalability and resource efficiency: Processes large HTS datasets in hours rather than weeks while reducing memory usage.

Scientific Applications:

• Adaptive immunity research: Enables analysis of BCR diversity and evolution to study adaptive immune responses.
• Antibody drug development: Supports identification and characterization of antibody sequences relevant to therapeutic development.
• Disease immunology: Facilitates comparison of BCR repertoires to investigate immune changes in infections, cancer, and other diseases.

Methodology:

Computational steps explicitly include ultrafast multiple-sequence alignment of BCR/antibody sequences, extraction of B-cell receptors from HTS data, V and J gene assignment, clonotype analysis, mutation (somatic hypermutation) profiling, lineage tree construction, and repertoire comparison.