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

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


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.


The fasta files included are:

Oryza sativa:
    Based on ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.0/all.dir/all.pep ; 67393 sequences.
	Rice.pep.1.sptp.fasta        First gene models only, 56591 genes.
	Rice.pep.1.sptp.YES.fasta    A subset of the above; the 8071 genes with signal peptide predicted by SignalP.
	Rice.pep.1.sptp.YES.S.fasta  A subset of the above; the 5607 genes with signal peptide predicted by both SignalP, TargetP.

Arabidopsis thaliana:
	Tair8.pep.1.sptp.fasta        First gene models only; 27201 genes.
	Tair8.pep.1.sptp.YES.fasta    A subset of the above; 5194 genes with signal peptide predicted by SignalP.
	Tair8.pep.1.sptp.YES.S.fasta  A subset of the above; 4555 genes with signal peptide predicted by both SignalP, TargetP.

        Tair9.pep.sptp.fasta          33410 gene models.
        Tair9.pep.1.sptp.fasta        First gene models only, 27343 genes.
        Tair9.pep.1.sptp.YES.fasta    Subset of the above; 5226 genes with signal peptide predicted by SignalP.
        Tair9.pep.1.sptp.YES.S.fasta  Subset of the above; 4555 genes with signal peptide predicted by both SignalP, TargetP.  

Brachypodium distachyon:
        Brachy.pep.1.sptp.fasta       First gene models only, 25532 genes.
        Brachy.pep.1.sptp.YES.fasta   Subset of above; 4923 genes with signal peptide predicted by SignalP.
        Brachy.pep.1.sptp.YES.S.fasta Subset of above; 3689 genes with signal peptide predicted by both SignalP, TargetP.

Solanum Lycopersicum
        ITAG1.pep.sptp.fasta          33926 gene models.
        ITAG1.pep.sptp.YES.fasta      Subset of above; 5756 genes with signal peptide predicted by SignalP.
        ITAG1.pep.sptp.YES.S.fasta    Subset of above; 5051 genes with signal peptide predicted by both SignalP, TargetP.