CHfinder

CHFinder identifies exons encoding constant (C_H) domains of immunoglobulin heavy chains in jawed vertebrates, with a focus on Actinopterygii fish, to characterize IgM, IgD, and IgT genes for evolutionary and structural analyses.

Key Features:

• Domain Identification: Employs a custom bioinformatics pipeline integrated with machine learning techniques to identify exons coding for C_H domains in fish immunoglobulins.
• Immunoglobulin Isotypes Analysis: Analyzes teleost immunoglobulin isotypes IgM, IgD, and IgT, noting IgT as unique to teleosts.
• Phylogenetic Comparisons: Compares deduced amino acid sequences of IgT C_H1 exons with those of IgM to infer evolutionary relationships and origins distinct from recent duplication events in Actinopterygii.
• Novel Variant Discovery: Detects previously undescribed IgT variants in teleost and holostean fish.

Scientific Applications:

• Evolutionary Biology: Enables phylogenetic analysis of immunoglobulin gene evolution across fish species, including Actinopterygii.
• Immunogenetics: Supports characterization of immunoglobulin gene architecture and diversity in teleosts and holosteans.
• Comparative Genomics: Facilitates comparative studies of adaptive immunity genes in jawed vertebrates.

Methodology:

Uses a custom-developed bioinformatics pipeline integrated with machine learning techniques to identify exons coding for C_H domains and performs systematic comparisons of deduced amino acid sequences of IgT C_H1 exons with IgM.