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Protocols

SVARAP specifications

Information


Unique identifier OMICS_12902
Name SVARAP
Alternative name Sequence VARiability Analysis Program
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Other
Computer skills Medium
Version 2.1.2
Stability Stable
Requirements
Microsoft Excel, Clustal X alignment
Maintained No

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Publication for Sequence VARiability Analysis Program

SVARAP citations

 (3)
call_split

Core Gene Set As the Basis of Multilocus Sequence Analysis of the Subclass Actinobacteridae

2011
PLoS One
PMCID: 3069002
PMID: 21483493
DOI: 10.1371/journal.pone.0014792
call_split See protocol

[…] The common set of genes thus obtained were aligned using clustal X program, version 1.83, in the PHYLIP software package . New broad range primers were designed for amplification and sequencing using SVARAP software which analyzes and graphically represents the variability in stretches of 50-bp along the nucleotide sequence , . A BLAST search was performed to check potential primers for unspecific […]

library_books

Pepper Mild Mottle Virus, a Plant Virus Associated with Specific Immune Responses, Fever, Abdominal Pains, and Pruritus in Humans

2010
PLoS One
PMCID: 2850318
PMID: 20386604
DOI: 10.1371/journal.pone.0010041

[…] two different regions of the PMMoV genome were obtained by RT-PCR amplification using the SuperScript One-Step RT-PCR System (Invitrogen Life Technologies) and primers that had been designed with the SVARAP program . The first targeted region is located near the 5′ end of the genome (primers used are PMMoV5pFwd: 5′-ATATCTGATGATGCAAGTTC-3′, 348 (the primer location was defined in reference to seque […]

call_split

Sca1, a previously undescribed paralog from autotransporter protein encoding genes in Rickettsia species

2006
BMC Microbiol
PMCID: 1388218
PMID: 16504018
DOI: 10.1186/1471-2180-6-12
call_split See protocol

[…] To identify sca1 sequence fragments variable among Rickettsia species and useable as a PCR target, we used the Sequence Variability Analysis Program (SVARAP) software []. This software determines the genetic diversity among sequences using a sliding window analysis, by moving a window of 50 nucleotide position […]

Citations

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SVARAP institution(s)
Laboratoire de virologie, Fédération hospitalière de bactériologie-virologie clinique et d'hygiène, CHRU Timone, Marseille, France; Unité des Rickettsies, CNRS UMR 6020 IFR48, Faculté de médecine, Université de la Méditerranée, Marseille, France

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