SVARAP and aSVARAP: simple tools for quantitative analysis of nucleotide and amino acid variability and primer selection for clinical microbiology

BMC Microbiology
Philippe ColsonDidier Raoult

Abstract

Simple computerized methods that analyse variability along alignments of nucleotide or amino acid sequences can be very useful in a clinical microbiology laboratory for two main purposes. First, to optimize primer selection, which is critical for the identification of infectious pathogens based on gene sequencing: primers must target conserved nucleotide regions bordering highly variable areas to ensure discrimination of species. Second, it can be of interest to reveal mutations associated with drug resistance of pathogen agents. Our aim was therefore to test easy and cost-free tools (SVARAP and aSVARAP) that require short hands-on work, little expertise, and which allow visual interpretation and statistical analysis of results. We first tested SVARAP to improve a strategy of identification of streptococci species of the Viridans Group targeting the groESL gene. Two regions with < 500 nucleotides were identified, one being significantly more discriminant than one of a similar length used in a previous study (mean number of nucleotide differences between species, 113 (range: 12-193) vs. 77 (range: 14-109); p < 10-3). Secondly, aSVARAP was tested on reverse transcriptase (RT) sequences from 129 HIV-1 clinical strains to identify ...Continue Reading

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Citations

May 1, 2007·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Alicia N MassaCraig F Morris
Aug 2, 2013·Antonie van Leeuwenhoek·Joana BondosoOlga Maria Lage
Mar 1, 2006·BMC Microbiology·Maxime NgwamidibaPierre-Edouard Fournier
Mar 5, 2014·Canadian Journal of Microbiology·Marcela FresnoPatricio Retamal
Jan 15, 2013·Comparative and Functional Genomics·Haitham Sobhy, Philippe Colson
Jan 29, 2008·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Philippe ColsonRené Gérolami
Dec 3, 2008·Microbiology·Iskandar Ben SalahMichel Drancourt
Sep 19, 2006·FEMS Microbiology Letters·Bernard La ScolaDidier Raoult
Sep 16, 2017·Nucleic Acids Research·Nara LeeSeema S Lakdawala
Feb 2, 2020·Scientific Reports·Nisrine ChelkhaPhilippe Colson
Jul 19, 2012·Asian Pacific Journal of Tropical Medicine·Nabil Ben Salem AbidMahjoub Aouni
Mar 7, 2020·Journal of Clinical Microbiology·Anselme MillogoMichel Drancourt

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Datasets Mentioned

BETA
AF378195
AF378196
AF389515
AF378197
AF338228
AY38047
AF417589
AF389514
AF389516
AF117741

Methods Mentioned

BETA
PCR

Software Mentioned

Oligo Primer Analysis
aSVARAP ( for amino acid Sequence VARiability Analysis Program )
ClustalX
aSVARAP
Excel
SVARAP
AL2CO
SDRDP
SVARAP ( Sequence VARiability Analysis Program )
SWAN

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