Prediction of twin-arginine signal peptides. BMC Bioinformatics 6:167

Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800, Lyngby, Denmark.
BMC Bioinformatics (Impact Factor: 2.67). 02/2005; 6(1):167. DOI: 10.1186/1471-2105-6-167
Source: PubMed

ABSTRACT Proteins carrying twin-arginine (Tat) signal peptides are exported into the periplasmic compartment or extracellular environment independently of the classical Sec-dependent translocation pathway. To complement other methods for classical signal peptide prediction we here present a publicly available method, TatP, for prediction of bacterial Tat signal peptides.
We have retrieved sequence data for Tat substrates in order to train a computational method for discrimination of Sec and Tat signal peptides. The TatP method is able to positively classify 91% of 35 known Tat signal peptides and 84% of the annotated cleavage sites of these Tat signal peptides were correctly predicted. This method generates far less false positive predictions on various datasets than using simple pattern matching. Moreover, on the same datasets TatP generates less false positive predictions than a complementary rule based prediction method.
The method developed here is able to discriminate Tat signal peptides from cytoplasmic proteins carrying a similar motif, as well as from Sec signal peptides, with high accuracy. The method allows filtering of input sequences based on Perl syntax regular expressions, whereas hydrophobicity discrimination of Tat- and Sec-signal peptides is carried out by an artificial neural network. A potential cleavage site of the predicted Tat signal peptide is also reported. The TatP prediction server is available as a public web server at

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Available from: Jannick Bendtsen, Aug 22, 2015
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    • "The prediction of transmembrane helices was determined using TMHMM 2.0 (Krogh et al., 2001) software. Those four prediction tools were chosen among the others based on several comparative studies which describe them to give the best predictions (Möller et al., 2001; Bendtsen et al., 2005; Rahman et al., 2008; Ravipaty and Reilly, 2010). When a transmembrane helix was predicted to be present in the signal sequence, it was considered as a false prediction of the TMHMM 2.0 software (Emanuelsson et al., 2007). "
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