Searches for germline variable (V), diversity (D) and joining (J) genes matches for T-cell receptor (TCR) and immunoglobulin (IG) sequences using BLAST algorithm. Works both with amino-acid and nucleotide sequences and supports alignment to IMGT(R) germline sequence database, as well as custom databases. Provides information of CDR1,2 and FR1,2,3 region markup and germline sequence mutations.
Provides a suite of utilities that cover a range of complex analysis tasks for immunoglobulin (Ig) repertoire sequencing data. Change-O is a suite of utilities that (i) processes the output of V(D)J alignment tools, (ii) assigns clonal clusters to Ig sequences and (iii) reconstructs germline sequences. It also offers applications to import data from the frequently used IMGT/HighV-QUEST tool and a set of utilities to perform basic database operations, such as sorting, filtering and modifying annotations.
Allows summary, interrogation, and further processing of IMGT/HighV-QUEST output files. IgAT is a Microsoft Excel based software for the extensive analysis and graphical presentation of very large collections of immunoglobulin (Ig) transcripts which have been pre-analyzed by the web-based IMGT/HighV-QUEST program. It additionally calculates the probability of antigen-driven selection within Ig repertoires and predicts structural properties of the antigen-binding site.
Allows users to analyze T-cell antigen receptor (TCR) sequencing data. MiTCR is a program permitting the study of hundreds of millions of raw high-throughput sequencing reads containing sequences encoding human or mouse a or TCR chains. It also allows the extraction of -cell clones from next generation sequencing (NGS) data.
Enables users to assign V and J regions of immunoglobulin sequences to their corresponding germline alleles. IgSCUEAL aims to detect recombination breakpoints and affect germline genes from rearranged immunoglobulin genes. This tool utilizes a statistical model of sequence evolution permitting generation of a weighted set of assignments.
Utilizes re-alignment to identify V(D)J genes and alleles after common local alignment. A methodology is developed to correct the PCR and sequencing errors, and to minimize the PCR bias among various rearranged sequences with different V and J gene families. IMonitor provides general adaptation for sequences from all receptor chains of different species and outputs useful statistics and visualizations. Usefulness of IMonitor was demonstrated on minimal residual disease detection of patients with B-cell Acute Lymphoblastic leukemia.