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SPEP analysis

Signal peptides identify the destination of protein sequences, by promoting the translocation through cell membranes (inner membrane for gram negative). The signal peptides have a central hydrophobic core, a N-terminus part of polar or positive charged residues, and the C-terminus part (close to the cleavage site) polar or negative charged. Although Prokaryotes (gram positive and gram negative) and Eukaryotes signal peptides share this common features, their length distribution and hydrophobicity picks are particular of each class of organisms. We computed with the Kyte-Doolittle [6] hydrophobicity scale the average value ($h$) for each signal peptide position $i$ as
\begin{displaymath}
h_{av}(i)=1/(2W+1)\sum_{j=-W}^{W}h(i+j) \; .
\end{displaymath} (5)

where we set $W=9$. In this way we can identify the location of the maximum of $h_{av}$. In Table 2 we report the minimal, the maximal, the average length and the average position of the hydrophobic pick ($h_{av}$) for each organism. This simple analysis (confirmed also with a more thorough study, data not shown) indicates that a particular care should be used in the prediction of this sorting signal. In particular, we always train and evaluate the performance of our method using the subsets defined by the different types of organisms.
Table 2: Signal peptide lengths in different organisms

Organism
Average Minimal Maximal Hydrophobicity
  Length Length Length Maximal Position

Eukaryotes
22 7 56 13
Gram Positive 25 11 58 15
Gram Negative 33 21 63 19



Subsections
next up previous
Next: SignalNet and CleavageNet performance Up: SPEP: a Signal Peptide Previous: Neural Network System
2003-06-12