SHMTool: a webserver for comparative analysis of somatic hypermutation datasets

Abstract

The somatic hypermutation (SHM) of Immunoglobulin variable (V) regions is a key process in the generation of antibody diversity. The growing number of datasets of point mutations that occur during SHM in mice and humans often include comparisons between wild-type and individuals or strains genetically defective in the repair mechanisms that contribute to SHM. However, it has been difficult to compare the results of different studies because the analyses have not been standardized for criteria such as correction for base composition and the inclusion of unique mutations. If many mutations are involved, the analysis can also be time consuming. To overcome these problems and facilitate a standardized analysis and display of similar data, we present a webserver (SHMTool) for comparing SHM datasets, available at http://scb.aecom.yu.edu/shmtool.

Figure 1. Outline of SHMTool process

The raw CONTROL and CASE datasets (far left) require user preprocessing as described in text before submission to SHMTool. The webserver produces mutation counts and comparative statistics for both unique and non-unique mutations, as well as spatial plots. Optionally, a subregion S of the sequence can be analyzed separately and compared to its complementary subregion S’.