Computational protocol: Regulation of solvent tolerance in Pseudomonas putida S12 mediated by mobile elements

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Protocol publication

[…] All analysis was performed using geneious software (BioMatters, Auckland, New Zealand), unless otherwise stated in the text. BLAST search of insertion sequence ISS12 was performed at the NCBI website (Altschul et al., ). A query coverage of >70% and an e‐value > E−5 were used as cut‐off. The selected sequences were aligned using MAFFT (Katoh and Standley, ) or Muscle (Edgar, ); and phylogenetic trees were created using default settings of FastTree Builder (Price et al., ) integrated within the Geneious software. Phylogenetic trees were created using the ‘maximum likelihood’ and pseudocounts. The trees were visualized as cladogram in increasing order, and distances were computed in ‘number of base substitutions per site’. The ISFinder (Siguier et al., ) and ACLAME (Leplae et al., ) were used to identify additional insertion sequences. In addition, for the best matching identities, results were aligned using the available full sequences to get the percentage identity and to avoid information loss due to shorter homologous regions retained by a BLAST hit. […]

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