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    Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria

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    Publication date
    2008-11
    Author
    Rahman, O.
    Cummings, S.P.
    Harrington, Dean J.
    Sutcliffe, I.C.
    Keyword
    Lipoproteins; Signal peptides; Bioinformatics; Genomics; Firmicutes; Actinobacteria
    Peer-Reviewed
    Yes
    
    Metadata
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    Abstract
    Bacterial lipoproteins are a diverse and functionally important group of proteins that are amenable to bioinformatic analyses because of their unique signal peptide features. Here we have used a dataset of sequences of experimentally verified lipoproteins of Gram-positive bacteria to refine our previously described lipoprotein recognition pattern (G+LPP). Sequenced bacterial genomes can be screened for putative lipoproteins using the G+LPP pattern. The sequences identified can then be validated using online tools for lipoprotein sequence identification. We have used our protein sequence datasets to evaluate six online tools for efficacy of lipoprotein sequence identification. Our analyses demonstrate that LipoP (http://www.cbs.dtu.dk/services/LipoP/) performs best individually but that a consensus approach, incorporating outputs from predictors of general signal peptide properties, is most informative.
    URI
    http://hdl.handle.net/10454/11573
    Version
    No full-text in the repository
    Citation
    Rahman O, Cummings SP, Harrington DJ et al (2008) Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria. World Journal of Microbiology and Biotechnology. 24(11): 2377.
    Link to publisher’s version
    http://dx.doi.org/10.1007/s11274-008-9795-2
    Type
    Article
    Collections
    Life Sciences Publications

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