This result can be explained by the fact that standard parameters for V-QUEST allow more mutations in the DH-gene core.
TCR β-CDR3 mRNA sequences of human T-cell clones were collected from the public database of NCBI at NIH. Vβ-, Jβ-, Dβ-segments were identified using the V-QUEST algorithm from the international ImMunoGeneTics information system [13].
Results from JoinSolver were compared to those produced by the V-QUEST and JunctionAnalysis algorithms of the IMGT system [62], which also analyzes VH sequences for gene usage and somatic mutations.
However, differences between classes of MAbs were similar whether the comparisons were calculated using V-QUEST or JoinSolver, and these relative differences (e.g., the average CDR-H3 length of self vs. non-self MAbs) are the important parameters in our study.
The amino acid sequence of each CDR3 junction region was determined using V-Quest, allowing for indels.
Clonally related sequences were identified based on the DNA sequence of the CDR3 ('junction') region as reported by V-Quest.
V-QUEST, however, is based on the BLAST algorithm; it does not guarantee finding the best alignment of two sequences (Altschul et al., 1990).
There are several different approaches and corresponding programs available online for carrying out these analyses, including iHMMune, V-Quest, Joinsolver, and SoDA and SoDA2.
The V-quest package [ 16, 17] created and hosted by ImMunoGeneTics is a useful tool for medium-scale TCR-seq data handling and annotation.
Both JOINSOLVER and V-QUEST provide multiple gene segment possibilities but the implementation only provides junction analysis for the topmost choice.
SoDA's guarantee of optimality in the inferred rearrangement is obtained at the cost of computational effort; SoDA takes more CPU time than either JOINSOLVER or V-QUEST.
