rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses

Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The w...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Persson, Sofia [verfasserIn] Larsson, Christina Simonsson, Magnus Ellström, Patrik

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	Primer design Degenerate primers PCR RT-PCR qPCR Digital PCR Sequence variable virus Norovirus Genotyping

Anmerkung:	© The Author(s) 2022

Übergeordnetes Werk:	Enthalten in: BMC bioinformatics - London : BioMed Central, 2000, 23(2022), 1 vom: 18. Juni
Übergeordnetes Werk:	volume:23 ; year:2022 ; number:1 ; day:18 ; month:06

Links:	Volltext

DOI / URN:	10.1186/s12859-022-04781-0

Katalog-ID:	SPR050794256

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912			\|a GBV_ILN_4335
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allfields	10.1186/s12859-022-04781-0 doi (DE-627)SPR050794256 (SPR)s12859-022-04781-0-e DE-627 ger DE-627 rakwb eng Persson, Sofia verfasserin (orcid)0000-0003-2611-3030 aut rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. Primer design (dpeaa)DE-He213 Degenerate primers (dpeaa)DE-He213 PCR (dpeaa)DE-He213 RT-PCR (dpeaa)DE-He213 qPCR (dpeaa)DE-He213 Digital PCR (dpeaa)DE-He213 Sequence variable virus (dpeaa)DE-He213 Norovirus (dpeaa)DE-He213 Genotyping (dpeaa)DE-He213 Larsson, Christina aut Simonsson, Magnus aut Ellström, Patrik aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 23(2022), 1 vom: 18. Juni (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:23 year:2022 number:1 day:18 month:06 https://dx.doi.org/10.1186/s12859-022-04781-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 18 06
spelling	10.1186/s12859-022-04781-0 doi (DE-627)SPR050794256 (SPR)s12859-022-04781-0-e DE-627 ger DE-627 rakwb eng Persson, Sofia verfasserin (orcid)0000-0003-2611-3030 aut rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. Primer design (dpeaa)DE-He213 Degenerate primers (dpeaa)DE-He213 PCR (dpeaa)DE-He213 RT-PCR (dpeaa)DE-He213 qPCR (dpeaa)DE-He213 Digital PCR (dpeaa)DE-He213 Sequence variable virus (dpeaa)DE-He213 Norovirus (dpeaa)DE-He213 Genotyping (dpeaa)DE-He213 Larsson, Christina aut Simonsson, Magnus aut Ellström, Patrik aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 23(2022), 1 vom: 18. Juni (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:23 year:2022 number:1 day:18 month:06 https://dx.doi.org/10.1186/s12859-022-04781-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 18 06
allfields_unstemmed	10.1186/s12859-022-04781-0 doi (DE-627)SPR050794256 (SPR)s12859-022-04781-0-e DE-627 ger DE-627 rakwb eng Persson, Sofia verfasserin (orcid)0000-0003-2611-3030 aut rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. Primer design (dpeaa)DE-He213 Degenerate primers (dpeaa)DE-He213 PCR (dpeaa)DE-He213 RT-PCR (dpeaa)DE-He213 qPCR (dpeaa)DE-He213 Digital PCR (dpeaa)DE-He213 Sequence variable virus (dpeaa)DE-He213 Norovirus (dpeaa)DE-He213 Genotyping (dpeaa)DE-He213 Larsson, Christina aut Simonsson, Magnus aut Ellström, Patrik aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 23(2022), 1 vom: 18. Juni (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:23 year:2022 number:1 day:18 month:06 https://dx.doi.org/10.1186/s12859-022-04781-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 18 06
allfieldsGer	10.1186/s12859-022-04781-0 doi (DE-627)SPR050794256 (SPR)s12859-022-04781-0-e DE-627 ger DE-627 rakwb eng Persson, Sofia verfasserin (orcid)0000-0003-2611-3030 aut rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. Primer design (dpeaa)DE-He213 Degenerate primers (dpeaa)DE-He213 PCR (dpeaa)DE-He213 RT-PCR (dpeaa)DE-He213 qPCR (dpeaa)DE-He213 Digital PCR (dpeaa)DE-He213 Sequence variable virus (dpeaa)DE-He213 Norovirus (dpeaa)DE-He213 Genotyping (dpeaa)DE-He213 Larsson, Christina aut Simonsson, Magnus aut Ellström, Patrik aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 23(2022), 1 vom: 18. Juni (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:23 year:2022 number:1 day:18 month:06 https://dx.doi.org/10.1186/s12859-022-04781-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 18 06
allfieldsSound	10.1186/s12859-022-04781-0 doi (DE-627)SPR050794256 (SPR)s12859-022-04781-0-e DE-627 ger DE-627 rakwb eng Persson, Sofia verfasserin (orcid)0000-0003-2611-3030 aut rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. Primer design (dpeaa)DE-He213 Degenerate primers (dpeaa)DE-He213 PCR (dpeaa)DE-He213 RT-PCR (dpeaa)DE-He213 qPCR (dpeaa)DE-He213 Digital PCR (dpeaa)DE-He213 Sequence variable virus (dpeaa)DE-He213 Norovirus (dpeaa)DE-He213 Genotyping (dpeaa)DE-He213 Larsson, Christina aut Simonsson, Magnus aut Ellström, Patrik aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 23(2022), 1 vom: 18. Juni (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:23 year:2022 number:1 day:18 month:06 https://dx.doi.org/10.1186/s12859-022-04781-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 18 06
language	English
source	Enthalten in BMC bioinformatics 23(2022), 1 vom: 18. Juni volume:23 year:2022 number:1 day:18 month:06
sourceStr	Enthalten in BMC bioinformatics 23(2022), 1 vom: 18. Juni volume:23 year:2022 number:1 day:18 month:06
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Primer design Degenerate primers PCR RT-PCR qPCR Digital PCR Sequence variable virus Norovirus Genotyping
isfreeaccess_bool	true
container_title	BMC bioinformatics
authorswithroles_txt_mv	Persson, Sofia @@aut@@ Larsson, Christina @@aut@@ Simonsson, Magnus @@aut@@ Ellström, Patrik @@aut@@
publishDateDaySort_date	2022-06-18T00:00:00Z
hierarchy_top_id	326644814
id	SPR050794256
language_de	englisch
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Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. 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author	Persson, Sofia
spellingShingle	Persson, Sofia misc Primer design misc Degenerate primers misc PCR misc RT-PCR misc qPCR misc Digital PCR misc Sequence variable virus misc Norovirus misc Genotyping rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses
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topic_title	rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses Primer design (dpeaa)DE-He213 Degenerate primers (dpeaa)DE-He213 PCR (dpeaa)DE-He213 RT-PCR (dpeaa)DE-He213 qPCR (dpeaa)DE-He213 Digital PCR (dpeaa)DE-He213 Sequence variable virus (dpeaa)DE-He213 Norovirus (dpeaa)DE-He213 Genotyping (dpeaa)DE-He213
topic	misc Primer design misc Degenerate primers misc PCR misc RT-PCR misc qPCR misc Digital PCR misc Sequence variable virus misc Norovirus misc Genotyping
topic_unstemmed	misc Primer design misc Degenerate primers misc PCR misc RT-PCR misc qPCR misc Digital PCR misc Sequence variable virus misc Norovirus misc Genotyping
topic_browse	misc Primer design misc Degenerate primers misc PCR misc RT-PCR misc qPCR misc Digital PCR misc Sequence variable virus misc Norovirus misc Genotyping
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title	rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses
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title_full	rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses
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author_browse	Persson, Sofia Larsson, Christina Simonsson, Magnus Ellström, Patrik
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title_sort	rprimer: an r/bioconductor package for design of degenerate oligos for sequence variable viruses
title_auth	rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses
abstract	Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. © The Author(s) 2022
abstractGer	Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. © The Author(s) 2022
abstract_unstemmed	Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. © The Author(s) 2022
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title_short	rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses
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rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses

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