Computational protocol: Clustering subspecies of Aeromonas salmonicida using IS630 typing

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Protocol publication

[…] The hybridization patterns were scanned and the data were analyzed using the BioNumerics software version 6.6 (Applied Maths, Kortrijk, Belgium). Bands automatically assigned by the computer were checked visually and corrected manually. Cluster analysis of the IS-RFLP patterns was done by the unweighted pair group method with average linkages (UPGMA) using the Dice coefficient and the following parameters: 0.5% Optimization, 0% Band filtering, 0.5% Tolerance and ignore uncertain bands.Prediction of T3SS effectors was performed with the Modlab® online software (http://gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html) []. […]

Pipeline specifications

Software tools BioNumerics, T3SS_prediction
Application Protein sequence analysis
Organisms Aeromonas salmonicida