IgMAT

IgMAT annotates immunoglobulin (antibody) sequences from high-throughput sequencing datasets to map framework (FR) and complementarity-determining regions (CDRs) across diverse species.

Key Features:

• Species-Agnostic Annotation: Annotates antibody sequences from diverse species and accepts user-defined datasets to represent species-specific structural characteristics.
• Reduced Amino Acid Alphabet and HMM Alignments: Uses a reduced amino acid alphabet and combines multiple Hidden Markov Model (HMM) alignments into a single consensus model to improve annotation accuracy across species.
• Customizability: Allows users to add custom antibody sequence datasets for annotation of non-standard or underrepresented species.
• Output Formats: Generates output formats including BED files that contain coordinates for Framework (FR) and Complementarity-Determining Regions (CDR).

Scientific Applications:

• Immunogenetics: Supports immunogenetics studies requiring precise annotation of antibody regions.
• Immune Repertoire Profiling: Enables mapping of changes in polyclonal immune repertoires from high-throughput sequencing, including responses to disease and vaccination.
• Cross-Species Antibody Research: Facilitates analysis of antibody repertoires from non-model species by allowing custom datasets and species-agnostic annotation.

Methodology:

Implemented as a Python module that applies a reduced amino acid alphabet and integrates multiple HMM alignments into a consensus model for sequence annotation.