iSMART performs a specially parameterized pairwise local alignment on T cell receptor CDR3 sequences to group them into antigen-specific clusters. iSMART is developed by Bo Li ([email protected]), with all rights reserved. iSMART is under GPL3.0 license.

iSMART is written in Python2, and is portable without installations.

iSMART requires the following python package to run: Bio

To use iSMART, please put all the downloaded files into the same directory with the source code, and use the command line to run:

python iSMARTvx.py -f TCR_file ## Single file with variable gene

python iSMARTvx.py -f TCR_file -v ## Single file without variable gene

python iSMARTvx.py -d TCR_directory ## All files in a directory with variable gene. In this mode, after iSMART analyzes individual files, it performs cross comparisons between the CDR3 clusters identified from different individuals, and create a master table of shared CDR3s.

Input file format (in the order of columns):

CDR3 amino acid sequence (Starting from C, ending with the first F/L in motif [FL]G.G)

Variable gene name in Imgt format: TRBVXX-XX*XX

Joining gene name (optional)

Frequency (optional)

Other information (optional)