Computational protocol: Large scale analysis of amino acid substitutions in bacterial proteomics

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Protocol publication

[…] Genomes of H. pylori clinical isolates were sequenced using GS Junior genome sequencer (Roche 454 Life Science, USA) for the strain A45 and Ion PGM sequencer system (Applied Biosystems, USA) for the strains E48 and H13-1. Whole genome sequencing of the N. gonorrhoeae clinical isolates was performed on GS FLX+ genome sequencer (Roche 454 Life Science, USA) using a standard protocol for a ”shotgun” genomic library. The raw reads were subject to correction using SAET 3, and Newbler v.2.6 (Roche 454 Life Science, USA) was used for assembly de novo. To yield a consistent annotation across all genomes in the study, the genomes were reannotated using a Prokka-based workflow []. To include possibly missing annotations of the WGS genomes, Artemis [] (release 16) was used to annotate all the ORFs including those located at the ends of the contigs [...] Analyses were conducted in R [] with the “phangorn” [], and “data.table” [] packages. Spectral library creation and filtration were performed with an ad hoc perl scripts included in speptide source code. […]

Pipeline specifications

Software tools Newbler, Prokka, Phangorn
Applications Phylogenetics, WGS analysis
Organisms Helicobacter pylori, Neisseria gonorrhoeae, Escherichia coli
Diseases Multiple Sclerosis
Chemicals Amino Acids