sigcleave predicts the site of cleavage between a signal sequence and the mature exported protein using the method of von Heijne. It reads one or more protein sequences and writes a standard EMBOSS report with the position, length and score of each predicted signal sequence. Optionally, you may specify the sequence is prokaryotic and this will change the default scoring data file used. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins.
sigcleave uses the method of von Heijne as modified by von Heijne in his later book where treatment of positions -1 and -3 in the matrix is slightly altered (see references). The minimum scoring weight value (-minweight) for the predicted cleavage site is specified. The value of -minweight should be at least 3.5. At this level, the method should correctly identify 95% of signal peptides, and reject 95% of non-signal peptides. The cleavage site should be correctly predicted in 75-80% of cases.
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By default sigcleave writes a 'motif' report file.
Here is the default file for eukaryotic signals:
# Amino acid counts for 161 Eukaryotic Signal Peptides, # from von Heijne (1986), Nucl. Acids. Res. 14:4683-4690 # # The cleavage site is between +1 and -1 # Sample: 161 aligned sequences # # R -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 +1 +2 Expect # - --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ------ A 16 13 14 15 20 18 18 17 25 15 47 6 80 18 6 14.5 C 3 6 9 7 9 14 6 8 5 6 19 3 9 8 3 4.5 D 0 0 0 0 0 0 0 0 5 3 0 5 0 10 11 8.9 E 0 0 0 1 0 0 0 0 3 7 0 7 0 13 14 10.0 F 13 9 11 11 6 7 18 13 4 5 0 13 0 6 4 5.6 G 4 4 3 6 3 13 3 2 19 34 5 7 39 10 7 12.1 H 0 0 0 0 0 1 1 0 5 0 0 6 0 4 2 3.4 I 15 15 8 6 11 5 4 8 5 1 10 5 0 8 7 7.4 K 0 0 0 1 0 0 1 0 0 4 0 2 0 11 9 11.3 L 71 68 72 79 78 45 64 49 10 23 8 20 1 8 4 12.1 M 0 3 7 4 1 6 2 2 0 0 0 1 0 1 2 2.7 N 0 1 0 1 1 0 0 0 3 3 0 10 0 4 7 7.1 P 2 0 2 0 0 4 1 8 20 14 0 1 3 0 22 7.4 Q 0 0 0 1 0 6 1 0 10 8 0 18 3 19 10 6.3 R 2 0 0 0 0 1 0 0 7 4 0 15 0 12 9 7.6 S 9 3 8 6 13 10 15 16 26 11 23 17 20 15 10 11.4 T 2 10 5 4 5 13 7 7 12 6 17 8 6 3 10 9.7 V 20 25 15 18 13 15 11 27 0 12 32 3 0 8 17 11.1 W 4 3 3 1 1 2 6 3 1 3 0 9 0 2 0 1.8 Y 0 1 4 0 0 1 3 1 1 2 0 5 0 1 7 5.6
Signal peptides mediate translocation across the endoplasmic reticulum (ER) membrane in eukaryotes. In prokaryotes signal peptides mediate translocation across the inner and outer membranes.
sigcleave may predict any number of cleavage sites in a protein sequence but not all of these will be biologically relevant; the prediction algorithm is not perfect. There is no cutoff to eliminate sites because it is down to human expertise to decide what is relevant or not. Although the end of a protein sequence is usually easy to predict from a nucleotide sequence, the same cannot be said for the start which depends on such things as promoters, transcriptional control and splicing. This is why all predicted cleavage sites are reported.
It is often useful to specify to use just the starting region of the input sequence using the in-built qualifier -send. For example, adding -send 50 to the command-line will check only the first 50 residues.
Original program "SIGCLEAVE" (EGCG 1989) by