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This map represents all the scientific publications referring to IgBLAST per scientific context
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Protocols

IgBLAST specifications

Information


Unique identifier OMICS_06083
Name IgBLAST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_06083
Name IgBLAST
Interface Web user interface
Restrictions to use None
Biological technology Illumina, Roche
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Publication for IgBLAST

IgBLAST citations

 (165)
library_books

Vaccine elicited receptor binding site antibodies neutralize two New World hemorrhagic fever arenaviruses

2018
Nat Commun
PMCID: 5951886
PMID: 29760382
DOI: 10.1038/s41467-018-04271-z

[…] nical limitations, the possibility that some cells encoded IgA instead of IgG (we only selected for IgM− cells), or false positive events in the flow cytometry. After sequencing PCR products, we used IgBLAST (http://www.ncbi.nlm.nih.gov/igblast) and IMGT® (http://www.imgt.org) to analyze IgG gene usage and the extent of VH/Vκ somatic hypermutation. We then cloned the PCR amplified variable segment […]

call_split

Sequence Based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen Specific Antibodies

2018
Front Immunol
PMCID: 5928204
PMID: 29740455
DOI: 10.3389/fimmu.2018.00889
call_split See protocol

[…] nerated an output of the translated amino acid protein sequence encoded by the open reading frame. We then aligned all of the protein sequences to the set of human germline IGHV genes from IMGT using IGBLAST. Based on the protein alignments and the IMGT coordinate system, we then determined the framework and CDR regions of the full heavy chain variable region protein sequence. Based on the CDR and […]

library_books

KSHV induces immunoglobulin rearrangements in mature B lymphocytes

2018
PLoS Pathog
PMCID: 5919685
PMID: 29659614
DOI: 10.1371/journal.ppat.1006967

[…] sorted single cells analyzed in to sequence Igλ variable regions from control (Mock Igλ+) and KSHV-revised (Igκ+ at infection, GFP+ Igκ-Igλ+ at 7dpi) lymphocytes and determined IGLV gene usage using IgBLAST. As expected[], control Igλ clones were biased towards IGLV gene families 1–3 with few clones utilizing IGLV4-10. In contrast, KSHV-modified Igλ+ cells displayed increased usage of upstream IG […]

library_books

Structure function analysis and therapeutic efficacy of antibodies to fungal melanin for melanoma radioimmunotherapy

2018
Sci Rep
PMCID: 5882926
PMID: 29615812
DOI: 10.1038/s41598-018-23889-z

[…] or the selection of positive transformants. Selected colonies were picked and analyzed through sequencing by both vbase2 (http://www.vbase2.org/vbase2.php) and NCBI blast (http://www.ncbi.nlm.nih.gov/igblast/). Sequences of the mAbs were compared by Clustal Omega (http://www.ebi.ac.uk/Tools/psa/emboss_needle/). […]

library_books

5′ Rapid Amplification of cDNA Ends and Illumina MiSeq Reveals B Cell Receptor Features in Healthy Adults, Adults With Chronic HIV 1 Infection, Cord Blood, and Humanized Mice

2018
Front Immunol
PMCID: 5879793
PMID: 29632541
DOI: 10.3389/fimmu.2018.00628

[…] sis, we also included reads with partial barcode (minimum 4 bp) and the adjacent 4-bp primer sequence. In indexed library runs, reads with a minimum 8-bp primer sequence were also included.(2)initial IGBLAST to identify BCR reads and join paired-ends: to remove non-BCR reads, we ran an initial in-house IGBLAST using a germline database of only functional V-genes from IMGT, rejecting reads with a b […]

library_books

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single cell RNA seq data

2018
Genome Med
PMCID: 5859752
PMID: 29558968
DOI: 10.1186/s13073-018-0528-3

[…] ) reference genome, all reads mapping to an annotated, non-immunoglobulin gene were discarded, and the remaining reads were retained for assembly. For annotation, we used the sequences available from IgBLAST (original source []).Fig. 7We sequenced 42 plasmablasts, 33 splenic germinal center (GC) B cells, and 33 memory B cells, the latter of which were purified based on their specificity for epitop […]


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IgBLAST institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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