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BASELINe specifications

Information


Unique identifier OMICS_08916
Name BASELINe
Alternative name Bayesian estimation of Antigen-driven SELectIoN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Steven Kleinstein

Information


Unique identifier OMICS_08916
Name BASELINe
Alternative name Bayesian estimation of Antigen-driven SELectIoN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.3
Stability Stable
Maintained Yes

Maintainer


  • person_outline Steven Kleinstein

Publications for Bayesian estimation of Antigen-driven SELectIoN

BASELINe citations

 (6)
library_books

Acquisition of N Glycosylation Sites in Immunoglobulin Heavy Chain Genes During Local Expansion in Parotid Salivary Glands of Primary Sjögren Patients

2018
Front Immunol
PMCID: 5890187
PMID: 29662487
DOI: 10.3389/fimmu.2018.00491

[…] Selection pressure analysis of the IGHV sequences belonging to a dominant clone was studied using the online Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences (BASELINe) program. This program uses statistical algorithms based on analysis of somatic mutation patterns of the IGHV sequ […]

library_books

Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths

2017
Front Immunol
PMCID: 5694033
PMID: 29180996
DOI: 10.3389/fimmu.2017.01433

[…] 0 sequences), IGHV3-23 (n = 60 sequences), IGHV4-39 (n = 50 sequences), IGHV5-51 (n = 60 sequences), and IGHV6-1 (n = 60 sequences) were analyzed for evidence of positive and negative selection using Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences (BASELINe, version 1.3) using a web-based interface. Focused selection statistics and the Human S5F somatic hypermutation ta […]

library_books

Human IgG2 and IgG4 expressing memory B cells display enhanced molecular and phenotypic signs of maturity and accumulate with age

2017
Immunol Cell Biol
PMCID: 5636940
PMID: 28546550
DOI: 10.1038/icb.2017.43

[…] V-gene nucleotides. The IgG receptor subclasses were determined using the IGH reference sequence (NG_001019). Selection for replacement mutations in framework regions (FR) and CDR was analyzed using Bayesian estimation of Antigen-driven SELectIoN (BASELINe; http://selection.med.yale.edu/baseline/)., […]

library_books

Transcriptomic analysis of common carp anterior kidney during Cyprinid herpesvirus 3 infection: Immunoglobulin repertoire and homologue functional divergence

2017
Sci Rep
PMCID: 5288646
PMID: 28148967
DOI: 10.1038/srep41531

[…] ction phases was conducted using testDiversity in Alakazam v.0.2.3 with 1000 bootstrap replicates. The selection pressure on Ig transcripts was estimated using observed and expected mutations and the Bayesian estimation of Antigen-driven SELectIoN (BASELINe) algorithm. To examine positions of diversity within the V region, a global alignment of Ig transcripts was performed using clustalW, and the […]

library_books

Evaluation of the Antigen Experienced B Cell Receptor Repertoire in Healthy Children and Adults

2016
Front Immunol
PMCID: 5066086
PMID: 27799928
DOI: 10.3389/fimmu.2016.00410

[…] cy of antigen-selected sequences increased in young children. From 6 years of age onward, the frequency of antigen-selected sequences was around 40% in both IGG and IGA transcripts (Figures A,B). The Bayesian estimation of antigen-driven SELectIoN (BASELINe) program uses a similar approach but compares for each transcript the expected mutations based on random distribution of the observed mutation […]

call_split

B Cell Dysregulation in Crohn's Disease Is Partially Restored with Infliximab Therapy

2016
PLoS One
PMCID: 4965034
PMID: 27468085
DOI: 10.1371/journal.pone.0160103
call_split See protocol

[…] for sequencing on an ABIPRISM 3130XL (Applied Biosystems, Carlsbad, CA). Obtained sequences were analyzed with IMGT database (http://imgt.cines.fr), Joinsolver (https://joinsolver.niaid.nih.gov) and Bayesian estimation of Antigen-driven SELectIoN (BASELINe; http://selection.med.yale.edu/baseline/). IgA and IgG receptor subclasses were determined using the IGH reference sequence (NG_001019). […]

Citations

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BASELINe institution(s)
Department of Pathology, Yale University School of Medicine, New Haven, CT; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
BASELINe funding source(s)
National Institutes of Health (NIH) [R03AI092379-01]; Yale University Biomedical High Performance Computing Center (NIH) [RR19895]

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