Computational protocol: Evaluation of Staphylococcus aureus Lipoproteins: Role in Nutritional Acquisition and Pathogenicity

Similar protocols

Protocol publication

[…] We collected all the predicted Lpp generated by different programs, for example Hidden Markov Model (Bagos et al., ), LipoP (Juncker et al., ), G+LPP (Sutcliffe and Harrington, ), G+LPPv2 (Rahman et al., ), LIPPREP (Taylor et al., ), Dolop (Babu et al., ), and Von Heijne (von Heijne, ). These lipoproteins were screened carefully by combination of the different values including hydrophobic plot (http://gcat.davidson.edu/DGPB/kd/kyte-doolittle.htm), lipobox sequence (http://www.mrc-lmb.cam.ac.uk/genomes/dolop/lipobox.shtml) and the cleaving site by PREP-LIPO (http://bioinformatics.biol.uoa.gr/PRED-LIPO/) or LipoP (http://www.cbs.dtu.dk/services/LipoP/). All Lpp sequences were blasted with other staphylococcal species and other genera by following programs NCBI protein blast (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) or KEGG (http://www.genome.jp/kegg/ko.html). […]

Pipeline specifications

Software tools LipoP, PRED-LIPO
Databases DOLOP
Application Protein sequence analysis
Organisms Staphylococcus aureus