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Biochem Biophys Res Commun. 2007 Jun 8;357(3):633-40. Epub 2007 Apr 5.

Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides.

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Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA.


We have developed an automated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequences. It is a 2-layer predictor: the 1st-layer prediction engine is to identify a query protein as secretory or non-secretory; if it is secretory, the process will be automatically continued with the 2nd-layer prediction engine to further identify the cleavage site of its signal peptide. The new predictor is called Signal-CF, where C stands for "coupling" and F for "fusion", meaning that Signal-CF is formed by incorporating the subsite coupling effects along a protein sequence and by fusing the results derived from many width-different scaled windows through a voting system. Signal-CF is featured by high success prediction rates with short computational time, and hence is particularly useful for the analysis of large-scale datasets. Signal-CF is freely available as a web-server at or

[Indexed for MEDLINE]

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