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 No

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Publication for VDJFasta

VDJFasta in publications

 (8)
PMCID: 5810246
PMID: 29472918
DOI: 10.3389/fimmu.2018.00118

[…] 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 […]

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

[…] amplified libraries and subjected to emulsion pcr and unidirectional sequencing using the gs flx titanium lib-l chemistry (454 sequencing, roche)., 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 […]

PMCID: 5187582
PMID: 28000661
DOI: 10.1038/ncomms13838

[…] flx technology using titanium long-read chemistry. read counts per sample are listed in ., 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 […]

PMCID: 5120205
PMID: 27857134
DOI: 10.1038/ncomms13376

[…] 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 […]

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 vā€‰+ā€‰jā€‰+ā€‰c […]


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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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