Computational protocol: The dissemination of C10 cysteine protease genes in Bacteroides fragilis by mobile genetic elements

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Protocol publication

[…] Members of the C10 protease family in B. fragilis were detected by BLAST analysis []. Sequences were aligned by CLUSTAL W [] or T-Coffee []. Protein secondary structure was predicted using GorIV [] and JPred []. Protein export signals were identified using the algorithms using LipPred [], LipoP [], SignalP [] and PSORTb []. Phylogenetic and molecular evolutionary analyses were conducted using genetic-distance-based neighbour-joining algorithms [] within MEGA Version 4.0 http://www.megasoftware.net/. Bootstrap analysis for 1000 replicates was performed to estimate the confidence of tree topology []. MegaBLAST [] was used to search all NCBI genomes for Bfgi1 and Bfgi2. […]

Pipeline specifications

Software tools Clustal W, T-Coffee, JPred, LipoP, SignalP, PSORTb, MEGA, BLASTN
Applications Phylogenetics, Protein sequence analysis
Organisms Streptococcus pyogenes, Bacteroides fragilis, Homo sapiens, Bacteroides fragilis 638R
Diseases Bacteroides Infections
Chemicals Cysteine