V(H) Replacement Footprint Analyzer-I, a Java-Based Computer Program for Analyses of Immunoglobulin Heavy Chain Genes and Potential V(H) Replacement Products in Human and Mouse

V(H) replacement occurs through RAG-mediated secondary recombination between a rearranged V(H) gene and an upstream unrearranged V(H) gene. Due to the location of the cryptic recombination signal sequence (cRSS, TACTGTG) at the 3′ end of V(H) gene coding region, a short stretch of nucleotides from the previous rearranged V(H) gene can be retained in the newly formed V(H)–D(H) junction as a “footprint” of V(H) replacement. Such footprints can be used as markers to identify Ig heavy chain (IgH) genes potentially generated through V(H) replacement. To explore the contribution of V(H) replacement products to the antibody repertoire, we developed a Java-based computer program, V(H) replacement footprint analyzer-I (V(H)RFA-I), to analyze published or newly obtained IgH genes from human or mouse. The V(H)RFA-1 program has multiple functional modules: it first uses service provided by the IMGT/V-QUEST program to assign potential V(H), D(H), and J(H) germline genes; then, it searches for V(H) replacement footprint motifs within the V(H)–D(H) junction (N1) regions of IgH gene sequences to identify potential V(H) replacement products; it can also analyze the frequencies of V(H) replacement products in correlation with publications, keywords, or V(H), D(H), and J(H) gene usages, and mutation status; it can further analyze the amino acid usages encoded by the identified V(H) replacement footprints. In summary, this program provides a useful computation tool for exploring the biological significance of V(H) replacement products in human and mouse.