IgBLAST: an immunoglobulin variable domain sequence analysis tool

Abstract

The variable domain of an immunoglobulin (IG) sequence is encoded by multiple genes, including the variable (V) gene, the diversity (D) gene and the joining (J) gene. Analysis of IG sequences typically requires identification of each gene, as well as a comparison of sequence variations in the context of defined regions. General purpose tools, such as the BLAST program, have only limited use for such tasks, as the rearranged nature of an IG sequence and the variable length of each gene requires multiple rounds of BLAST searches for a single IG sequence. Additionally, manual assembly of different genes is difficult and error-prone. To address these issues and to facilitate other common tasks in analysing IG sequences, we have developed the sequence analysis tool IgBLAST (http://www.ncbi.nlm.nih.gov/igblast/). With this tool, users can view the matches to the germline V, D and J genes, details at rearrangement junctions, the delineation of IG V domain framework regions and complementarity determining regions. IgBLAST has the capability to analyse nucleotide and protein sequences and can process sequences in batches. Furthermore, IgBLAST allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene.

B-cell tumor development in Tet2-deficient mice

“…PCR fragments were sequenced using the same VH family primer used for amplification. Sequences were analyzed using IgBlast 23 and International ImMunoGeneTics (IMGT) V-Quest, [24][25][26] and IgH V, D, and J genes with highest significance in both analyses are shown in Table 1.…”

Characterization of the B-cell receptor repertoires in peanut allergic subjects undergoing oral immunotherapy

“…Further optimization of the parameters as well as further update of sequencing technology, including sequence read length and quality, will be required to improve accurate clonotype assignments. In addition, our method has potential to obtain the full-length sequences of BCR transcripts, including those resulted from unexpectedly aberrant splicing or rearrangement, and those containing potentially novel exons that are not reported in the human genome reference database, whereas other previously reported algorithms such as IMGT/HighV-QUEST [27], IgBLAST [28], and MiXCR [20], use the information of only V(D)J regions. Indeed, we identified the reads that unexpectedly mapped to IGHV region with a deletion in a known V segment as shown in Fig.…”

Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

“…A variety of programs have been developed for high-throughput V(D)J gene assignment, as well as CDR3 identification and characterization, including international ImMunoGeneTics information system (IMGT)/HighV-QUEST, IgBLAST, JoinSolver, Ig analysis tool (IgAT), and Vidjil (2)(3)(4)(5)(6). Other tools can be used to define clones in the repertoire (Change-O) (4) or analyze Ag selection (IgAT and BASELINe) (5,7) or CSR (8).…”