Computational protocol: Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates

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Protocol publication

[…] The sequence data were aligned and manipulated in Gap4 (), genes were predicted using Glimmer3 () and visualized and curated in Artemis (), and conserved domains were identified using MotifScan (). Insertion sequences were identified using the IS Finder database (). Alignments and trees were constructed using Muscle () and Seaview (), respectively. Trees were created using the Bio-NJ Jukes–Cantor distance method. […]

Pipeline specifications

Software tools Glimmer, MUSCLE, SeaView
Application Nucleotide sequence alignment
Organisms Streptococcus pneumoniae
Diseases Pneumococcal Infections