IgBLAST: an immunoglobulin variable domain sequence analysis tool

By Jian Ye, Ning Ma, Thomas L. Madden, James Ostell. Nucleic Acids Res., 2013

1,151 citations recorded by the source corpus.

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.

Subfields: Immunology, Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/dca61bed30f62003dff3bfa89c10b8bd392f9837

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Citations in the corpus

Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences (2021, methodology): “1.(31) For IgBLASTn, the VDJ germline databases for human, mouse, rat, rabbit, and monkey were created using ImMunoGeneTics (IMGT) germline sequences derived from IMGT.”
Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires (2016, methodology): “Illumina sequences were quality-filtered and annotated using both the IMGT (60) and National Center for Biotechnology Information IgBlast software (61) with a CDR3 motif identification algorithm (62).”
Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells (2020, neutral): “0 (Ye et al., 2013) against the germline reference (202007-1 release) downloaded from the international ImMunoGeneTics information system (IMGT) (Giudicelli et al.”
T cell fate and clonality inference from single cell transcriptomes (2016, methodology): “To do this for the reconstructed TCR sequences we first converted them to entirely full-length sequences by using full-length V and J gene sequences from IMGT appropriate to the gene segments assigned by IgBLAST.”
Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8 (2016, methodology): “As before, the pipeline consists of the following five steps: (i) filter out reads with less than 300 nt; (ii) assignment of variable (V), diverse (D), and joining (J) gene families and alleles to each sequence using an in-house implementation of IgBlast [31] (sequences with E value> 10−3 for V or J”
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity (2016, neutral): “Therefore, in order to identify the ensemble of bnAbs from the whole donor Ab repertoire, we used the IgBLAST platform [27] to assess both germline gene of origin and productivity.”
Database resources of the National Center for Biotechnology Information (2020, background): “We have added several new features to IgBLAST (19).”
A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations (2020, methodology): “V(D)J gene segment and CDR3 sequences were determined by IgBlast (Ye et al., 2013) and/or IMGT/V-QUEST (Brochet et al., 2008).”
Antibody modeling using the Prediction of ImmunoGlobulin Structure (PIGS) web server (2014, methodology): “In brief, to build the HMM for aligning the heavy chains, we retrieved and aligned 37,182 sequences of immunoglobulin heavy and light ( κ and λ type) chains from Homo sapiens and Mus musculus from the National Center for Biotechnology Information (NCBI) database using IgBlast 64 .”
Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination (2021, neutral): “0 (50) for gene identification and align-”
Database resources of the National Center for Biotechnology Information. (2019, background): “IgBLAST (21) can now detect Ig rearrangements with ultra-long D and N regions such as those found in human anti-HIV antibodies.”
Multiple early factors anticipate post-acute COVID-19 sequelae (2022, neutral): “Somatic hypermutation rates (SHM) were deﬁned as the percentages of gaps and mismatches in the variable region of the query contig sequence compared to the top germ-line V gene hit identiﬁed through IgBLAST (Ye et al., 2013).”