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VDJFasta specifications

Information


Unique identifier OMICS_00004
Name VDJFasta
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License Academic Free License version 3.0
Computer skills Advanced
Version 1.1.2
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Jaume Pons
  • person_outline Arvind Rajpal

Publication for VDJFasta

VDJFasta citations

 (8)
library_books

Next Generation Sequencing of Antibody Display Repertoires

2018
Front Immunol
PMCID: 5810246
PMID: 29472918
DOI: 10.3389/fimmu.2018.00118

[…] rkov model (HMM) that captures the conserved sequences upstream and downstream of the CDR3 (). N2GSAb can rapidly identify germline and VH CDR3 and provides a tool for clustering unique sequences (). VDJFasta uses an HMM to accurately predict all VH and VL CDRs, as well as the GS linker sequence for scFv fragments, and can generate library diversity plots (). The ImmuneDB package aligns sequences […]

library_books

A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next Gen Immune Repertoire Sequencing Data

2017
Sci Rep
PMCID: 5509648
PMID: 28706301
DOI: 10.1038/s41598-017-04439-5

[…] The raw sequence output was analyzed using the VDJFasta algorithm; each sequence was annotated with IGHV and IGHJ germline segments and the amino acid sequence of the Complementary Determining Regions (CDRs). The CDR3 amino acid sequence was used […]

library_books

Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire

2016
Nat Commun
PMCID: 5187582
PMID: 28000661
DOI: 10.1038/ncomms13838

[…] IGHV, IGHD, IGHJ and CDR-H3 regions for each read was quality filtered, processed and annotated using the VDJFasta utility. Reference IGHV, IGHD and IGHJ genes from the international ImMunoGeneTics database were used. Mann-Kendall tests were performed in Matlab, against the null hypothesis of no trend (al […]

library_books

Germline encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire

2016
Nat Commun
PMCID: 5120205
PMID: 27857134
DOI: 10.1038/ncomms13376

[…] d from 454 high-throughput sequencing of the donor's memory B cell repertoire and from the corresponding single-cell cloning. The VDJ segments and VH CDR3 of each clone were first identified by using VDJFasta. Sequences were clustered into each clonal lineage using the VDJFasta single linkage method described previously. For tree topology representation of the memory B cell repertoire, somatic hyp […]

library_books

IGHV1 69 polymorphism modulates anti influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity

2016
Sci Rep
PMCID: 4754645
PMID: 26880249
DOI: 10.1038/srep20842

[…] DNA barcodes, converted from fastq to fasta and paired-end assembled. Barcode and primer sequences in the V-segment were then removed from all reads. Sequences were then processed using the AbGenesis VDJFasta pipeline to identify V,D,J segments, isotype, and translated CDRs, as previously described. Samples were rendered clonally non-redundant to include one unique representative of each V + J + C […]

library_books

A Highly Focused Antigen Receptor Repertoire Characterizes γδ T Cells That are Poised to Make IL 17 Rapidly in Naive Animals

2015
Front Immunol
PMCID: 4370043
PMID: 25852688
DOI: 10.3389/fimmu.2015.00118

[…] ed and de-convoluted using barcode identifiers at both ends of each sequence by a custom software pipeline to separate reads from every well in every plate. The resulting sequences are analyzed using VDJFasta (), which we have adapted to resolve barcodes and analyze sequences with a customized gene-segment database. The CDR3 nucleotide sequences are then extracted and translated. Barcode design is […]

Citations

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VDJFasta institution(s)
Research Informatics, Rinat-Pfizer Inc., South San Francisco, CA, USA; Protein Engineering, Rinat-Pfizer Inc., South San Francisco, CA, USA; Target Generation Unit, Pfizer Inc., South San Francisco, CA, USA

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