l         Secreted and/or transmembrane proteins are likely to be important in antigenic profile and contact with host cells because they are surface exposed.

l         In general, secreted and transmembrane proteins have signal peptide at the N-terminus.

l         Signal peptide has a common structure of a positively charged n-region followed by a hydrophobic h-region and a neutral but polar c-region.

l         Also, there is a (-3,-1) rule which is saying that residues at positions of –3 and –1 (relative to the cleavage site) must be small and neutral.

Signal output parsing

l         NN predictin score (neural network value)

l         HMM prediction score

l         Cleavage sites prediction by NN and HMM.

l         Criteria for a protein likely has signal peptide: NN and HMM scores are greater that 0.8; and cleavage sites predicted by both are the same.

Useful bio-home links:

l         ORF-finder at NCBI: http://www.ncbi.nlm.nih.gov/gorf/gorf.html;

l         GETORG: http://bioweb.pasteur.fr/seqanal/interfaces/getorf.html;

l         BLAST: http://www.ncbi.nlm.nih.gov/BLAST/;

l         Protein domain: Pfam: http://pfam.wustl.edu/hmmsearch.shtml;

l         SignalP2.0: http://www.cbs.dtu.dk/services/SignalP-2.0/#submission;

l         SignalP3.0: http://www.cbs.dtu.dk/services/SignalP/;

l         TRNAscan-SE: http://www.genetics.wustl.edu/eddy/tRNAscan-SE;