Computational protocol: Identification of a Novel Bacterial Outer Membrane Interleukin-1Β-Binding Protein from Aggregatibacter actinomycetemcomitans

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Protocol publication

[…] The SOSUI-GramN server [] was employed to predict the sub-cellular location of the protein. The sequence was analyzed using the SignalP 4.1 Server [] to predict the length of the signal sequence and the LipoP 1.0 Server [] to detect the presence of the lipoprotein signal sequence. Sequence similarity searches were performed with SIB using the BLAST network service. The SIB BLAST network service employs a server developed at SIB and NCBI BLAST 2 software []. Sequence alignments were performed using the Clustal W (1.83) program of the SIB T-Coffee multiple sequence alignment package []. […]

Pipeline specifications

Software tools SOSUI-GramN, SignalP, LipoP, BLASTN, Clustal W, T-Coffee
Application Protein sequence analysis
Organisms Aggregatibacter actinomycetemcomitans, Escherichia coli
Diseases Periodontitis
Chemicals Fluorescein-5-isothiocyanate