Computational protocol: Complete genome sequencing and analysis of a Lancefield group G Streptococcus dysgalactiae subsp. equisimilis strain causing streptococcal toxic shock syndrome (STSS)

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Protocol publication

[…] Transfer RNAs (tRNAs), transfer-messenger RNA (tmRNA), and rRNA sequences were predicted using ARAGORN []. Coding sequences (CDS) were predicted using in silico Molecular Cloning (In Silico Biology Inc., Yokohama City, Kanagawa, Japan) for selection of optimal start sites. Predicted genes and intergenic regions were compared using the NCBI sequence database http://blast.ncbi.nlm.nih.gov/Blast.cgi, and predicted CDS and start sites were adjusted accordingly. A genome-wide homology search was performed using the discontiguous megaBLAST algorithm http://blast.ncbi.nlm.nih.gov/Blast.cgi with a word size of 11 and rewards and penalties (2, -3) that optimize for alignments of about 85% identity. The phylogenetic tree of all sequenced Streptococcus species was constructed based on CVTree http://tlife.fudan.edu.cn/cvtree/[]. Secretion signal peptides were predicted using SignalP http://www.cbs.dtu.dk/services/SignalP[]. Sortases and cell wall sorting signals were predicted with available hidden Markov models using HMMER http://bamics3.cmbi.kun.nl/jos/sortase_substrates/help.html[]. Clustered, regularly interspaced, short palindromic repeat (CRISPR) spacers were detected using CRISPR Finder http://crispr.u-psud.fr/[]. The phylogenetic tree of all sequenced Streptococcus was constructed based on the CVTree http://tlife.fudan.edu.cn/cvtree/[] […]

Pipeline specifications

Software tools ARAGORN, CVTree, SignalP, HMMER
Databases tmRNA
Applications Genome annotation, Phylogenetics
Organisms Streptococcus dysgalactiae subsp. equisimilis, Streptococcus pyogenes, Homo sapiens
Diseases Streptococcal Infections, Alcohol-Related Disorders, Drug-Related Side Effects and Adverse Reactions
Chemicals Cysteine