Computational protocol: Clusters versus Affinity-Based Approaches in F. tularensis Whole Genome Search of CTL Epitopes

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Protocol publication

[…] Analysis of membrane protein topology was conducted by the program TMHMM v2.0 for prediction of transmembranal helices based on hidden Markov model. Analysis of proteins for presence of a signal peptide domain was performed by the Signalp 3.0 server . Proteins predicted to possess 10 or more predicted transmembranal domains (TM) and/or TMs spanning at least a third of the protein were assigned as membranal; Proteins predicted to possess less than 10 predicted TMs were assigned as partially membranal; proteins with no predicted transmembranal domains except signal peptide were assigned as “No TMs". […]

Pipeline specifications

Software tools TMHMM, SignalP
Application Membrane protein analysis
Organisms Francisella tularensis, Mus musculus