Immunoglobulin rearrangement identification software tools | Immune system data analysis
B cells express immunoglobulin (Ig) molecules on their outer surface and secrete them into the extracellular space. Secreted Ig is known as antibody. The genes that encode for antibodies are generated by many diversifying mechanisms including combinatorial rearrangement of gene segments, addition of non-templated (n) nucleotides at the junctions, and somatic hypermutation. This circumstance presents the important challenge of inferring the components of the original rearrangement for any observed Ig gene.
Identifies and delimits the variable (V), diversity (D) and joining (J) genes and alleles within immunoglobulin (Ig) or T-cell receptor (TR) nucleotide rearranged sequences. IMGT/V-QUEST delimits framework and complementarity determining regions. It then displays a graphical 2D representation of the variable region. It can also interact with additional IMGT tools for more detailed analysis via an option on the Search page for a detailed analysis, and via a link on the result page for the phylogenetic analysis of the variable region of input sequence.
Handles alignments with insertions/deletions (indels), while maintaining or improving the speed. HTJOINSOLVER is a desktop application, provided as an implementation of the partitioning method. Similar to the original JOINSOLVER algorithm, it conserves motifs to initiate the alignment process. The original algorithm was developed as a fast and accurate method, but was not designed to handle indels.
Allows modelling of processes implicated in human immunoglobulin heavy chain (IGH) gene rearrangement and maturation. iHMMune-align incorporates an explicit model of V-D-J recombination and somatic mutation processes in the form of a hidden Markov model (HMM). The software generates an alignment of the rearranged sequence with its most likely component germline genes. It includes an initial Smith–Waterman alignment step for identifying the IGHV gene. Two version are available: one for full-length or near full-length sequences and the other for short sequences.
Determines the rearrangement of antigen receptor based on somatic genetics of antibodies. Cloanalyst performs Bayesian and basic clonal analysis. The software can be useful for studying antibody somatic genetics.
Allows to proceed analysis of heavy chain joints. VDJsolver is based on a maximum-likelihood method which takes the lengths of the joint and the mutational status of the VH gene into account. It has a higher predictive performance for D-gene assignment in mutated and unmutated sequences than four other programs. It accepts bulk submissions and is able to analyse rearrangements to all the VH genes from the IMGT database.
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