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This directory contains gzipped fasta files for a few different genomes 
with added annotations about the secretion predictions
by the programs SecreTary, SignalP and TargetpP.

SecreTary is a new signal-peptide prediction program developed by the Secretom project. It was
developed primarily for use with plant genome data.

For details of the prediction programs TargetP and SignalP, see:
	Locating proteins in the cell using TargetP, SignalP, and related tools
	Olof Emanuelsson, Søren Brunak, Gunnar von Heijne, Henrik Nielsen
	Nature Protocols 2, 953-971 (2007).


Here is an example of a sequence-id line containing these secretion-related annotations:

>LOC_Os01g02160.1|13101.m00154|protein hydroxyproline-rich glycoprotein family protein, putative, expressed  signalPnn:0.935,YES,21  signalPhmm:1.000,0.000,SP,21  targetP:0.022,0.024,0.942,0.021,S,1  SecreTary:0.8375,pass

Interpretation of these annotations:

signalPnn:0.935,YES,21    these are results from the neural network part of signalp;
	Dscore = 0.935,
	YES a signal peptide is predicted (this is just based on the Dscore, YES iff Dscore >= 0.43)
	21 is the predicted length of the signal peptide. 

signalPhmm:1.000,0.000,SP,21   These are results from the hidden markov model part of signalp;
	1.000  is p_sp, the "probability" associated with the prediction that it is a signal peptide (SP).
	0.000  is p_sa, the "probability" associated with the prediction that it is a signal anchor (SA). 
	SP is the prediction. Look at p_sp, p_sa, and p_ns = 1 - (p_sp + p_sa); 
		predict SP, SA, or NS (not secreted) according to which of these three is greatest.
	21 is the predicted length of the SP or SA. 

targetP:0.022,0.024,0.942,0.021,S,1
	The first 4 numbers are scores for the 4 possible targetting predictions, 
		respectively C (chloroplast), M (mitochondia), S (secreted), and _ (other).
	S is the prediction, just based on which of the 4 scores is greatest.
	1 is a score in indicating the strength of the prediction, with 1 being strongest, and 5 weakest. 
		It is based on the difference between the two largest of the 4 targetting scores;
		i.e. a difference of 0.8-1.0 -> 1, 0.6-0.8 -> 2, etc.

SecreTary:0.8375,pass
        The signal peptide prediction program SecreTary gives a score of 0.8375; pass means it is predicted to be a signal-peptide, otherwise 'fail' would appear here. A score of >= 0.75 results in a 'pass'.

The gzipped fasta files included are:

Oryza sativa:
	TIGR6.1.STsptp.fa.gz

Arabidopsis thaliana:
	Tair10.STsptp.fa.gz

Brachypodium distachyon:
        Brachy1.2.STsptp.fa.gz

Solanum Lycopersicum
        ITAG2.STsptp.fa.gz

Populus trichocarpa
        Poptri2.STsptp.fa.gz