IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF)

INTRODUCTION IMGT/DomainGapAlign is the IMGT online tool for the analysis of amino acid (AA) sequences and two-dimensional (2D) structures of domains. The use of this tool is described here. Three domain types can be analyzed: the variable (V) and constant (C) domains of the immunoglobulins (IG) and T cell receptors (TR) and other immunoglobulin superfamily (IgSF) proteins, and the groove (G) domain of major histocompatibility (MH) and other MH superfamily (MhSF) proteins. IMGT/DomainGapAlign creates gaps in the user amino acid sequences and delimits, for the V and C domains, the framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT), and, for the G domains, the strands and helix, according to the IMGT unique numbering. The tool provides alignments with the closest sequences from the IMGT domain directory of IMGT/DomainDisplay. For the IG and TR V domains that result from V-(D)-J rearrangement, the tool provides alignments with the translation of the IMGT/GENE-DB germline V and joining (J) genes. IMGT/DomainGapAlign displays the amino acid changes, highlights them in IMGT Colliers de Perles, and provides tables with their detailed description, according to the IMGT rules. Several amino acid sequences can be analyzed simultaneously, provided that they belong to the same domain type.