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Protocols

AbMining ToolBox specifications

Information


Unique identifier OMICS_04063
Name AbMining ToolBox
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Csaba Kiss

Publication for AbMining ToolBox

AbMining ToolBox citations

 (4)
call_split

Many Routes to an Antibody Heavy Chain CDR3: Necessary, Yet Insufficient, for Specific Binding

2018
Front Immunol
PMCID: 5852061
PMID: 29568296
DOI: 10.3389/fimmu.2018.00395
call_split See protocol

[…] plicon libraries were processed using the Ion Xpress Amplicon library protocol and then prepared for sequencing on the Ion 316 Chip (Life Technologies). The sequences analysis was performed using the AbMining Toolbox as described by D’Angelo et al. (). […]

library_books

Next Generation Sequencing of Antibody Display Repertoires

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

[…] available to researchers, therefore, specialized pipelines for the analysis of recombinant antibody libraries, either naïve or in vitro selected against particular antigens, have been developed. The AbMining Toolbox is particularly suited for identifying VH CDR3, which is determined by using a hidden Markov model (HMM) that captures the conserved sequences upstream and downstream of the CDR3 (). […]

library_books

The dynamics of immunoglobulin V gene usage and clonotype expansion in mice after prime and boost immunizations as analyzed by NGS

2017
PMCID: 5718813
PMID: 29049006
DOI: 10.1080/21645515.2017.1379638

[…] s were downloaded from the Ion Torrent server (Thermo Fisher Scientific) after running the file generator plugin and reads over 400 bases long and with phred quality score >20 were selected using the AbMining toolbox suite. The output fasta file was split into blocks of 500,000 reads and submitted to the IMGT High V-quest server. The output data were clustered into clonotypes based on unique CDR3 […]

library_books

Engineering an Acinetobacter regulon for biosensing and high throughput enzyme screening in E. coli via flow cytometry

2014
Nucleic Acids Res
PMCID: 4081070
PMID: 24861620
DOI: 10.1093/nar/gku444

[…] t, Invitrogen). Each sample was prepared with a distinct barcode to allow a multiplex assay on a single Ion 316 chip (Life Technologies). The raw data from ion torrent sequencing was processed by the AbMining toolbox (). […]

Citations

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AbMining ToolBox institution(s)
New Mexico Consortium, Mexico

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