SONAR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SONAR
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Tool usage distribution map

This map represents all the scientific publications referring to SONAR per scientific context
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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 citations

 (4)
library_books

HIV specific Fc effector function early in infection predicts the development of broadly neutralizing antibodies

2018
PLoS Pathog
PMCID: 5908199
PMID: 29630668
DOI: 10.1371/journal.ppat.1006987

[…] equences 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 gp12 […]

library_books

Gene Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

2017
Front Immunol
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 (). […]

library_books

Historical changes of the Mediterranean Sea ecosystem: modelling the role and impact of primary productivity and fisheries changes over time

2017
Sci Rep
PMCID: 5349533
PMID: 28290518
DOI: 10.1038/srep44491

[…] ated as the product of the number of fishing vessels, kW per vessel (inferred from their GT), and the number of days spent fishing. To account for improvements in technology (e.g., mobile phone, GPS, sonar, radio) that were not captured by kW as a measure of effort (), a conservative technological “creep factor” of 1% as observed by Damalas et al. and EVOMED was applied from 1980 to 1995 while for […]

library_books

Antibodyomics: bioinformatics technologies for understanding B‐cell immunity to HIV‐1

2017
PMCID: 5516196
PMID: 28133812
DOI: 10.1111/imr.12480

[…] To add a temporal dimension to the analysis of B‐cell repertoires, we reimagined the Antibodyomics1 pipeline. Currently, the Software for Ontogenic aNalysis of Antibody Repertoires (SONAR; Antibodyomics2.1) provides a basis of Antibodyomics2. SONAR comprises a suite of tools for processing NGS data from B‐cell receptor libraries, including germline V(D)J gene annotation, lineage […]


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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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