SONAR protocols

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SONAR specifications

Information


Unique identifier OMICS_13855
Name SONAR
Alternative name Software for the Ontogenic aNalysis of Antibody Repertoires
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Software for the Ontogenic aNalysis of Antibody Repertoires

SONAR in pipeline

2017
PMCID: 5424261
PMID: 28539926
DOI: 10.3389/fimmu.2017.00537

[…] in order to ensure that our calculations were not affected by sequencing error from the 454 platform, we used a stringent quality control protocol as described in the following sections. we used sonar to assign germline v and j genes for each transcript (). sequences for which assignments could not be made were removed. in addition, transcripts contained stop codons or out-of-frame junctions […]


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SONAR in publications

 (2)
PMCID: 5908199
PMID: 29630668
DOI: 10.1371/journal.ppat.1006987

[…] from 10/13 bnab and 7/10 no-bnab individuals which were aligned using muscle (multiple sequence comparison by log- expectation https://www.ebi.ac.uk/tools/msa/muscle/). a script adapted from sonar (software for the ontogenic analysis of antibody repertoires) [] was adapted to calculate the percentage nucleotide differences of autologous viruses compared to the antigen sequences (conc […]

PMCID: 5424261
PMID: 28539926
DOI: 10.3389/fimmu.2017.00537

[…] is not sampled uniformly and that the sampling bias is gene specific and similar among donors and over time. the software for constructing and analyzing gssps is available from github as part of the sonar suite ()., to investigate the mutational space sampled by each germline v gene, we first compared the somatic mutations observed in human antibody repertoires of three healthy donors and three […]


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SONAR institution(s)
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
SONAR funding source(s)
This work was supported by the intramural program of the Vaccine Research Center, National Institute of Allergy, Infectious Disease, National Institutes of Health and HIVRAD grant AI104722-3 and U01 AI116086-01.

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