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.
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.
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.
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.
Permits the identification of immunoglobulin rearrangements. SoDA is a Hidden Markov Model (HMM) approach used to compute the posterior probabilities of candidate rearrangements and to find those with the highest values among them. The software has been validated on a set of simulated data, a set of clonally related sequences, and a group of randomly selected immunoglobulin (Ig) heavy chains from Genbank. Furthermore, the output format has been redesigned, in part, to facilitate comparison of multiple solutions.
Allows identification of sourcing gene segments in germline for rearranged antibodies. Ab-origin is a program based on BLAST that partitions functional antibody sequences to corresponding gene segments. The software allows detailed investigation of the original germline segment for antibodies and potential rearrangement profiles. It can be useful for the informatics study in the immune-community, so as to promote the understanding of antibody maturation process.
Allows to determine the minimal functional complexity of an antibody library. DEAL is based on a Polymerase Chain Reaction (PCR)-free Next Generation Sequencing (NGS) approach. It can take into account the sequencing error. The tool minimizes the possible confusion between the real base sequence variants from the background technical, taking into account both Phred derived error rate and Phi-X derived error rate.