Date : 2019

Author : Elise Gay

Input : JN3.proteins.fasta (Dutreux et al., 2018)

Output : effectorP.output / res_signalp / res_targetp / res_tmhmm / effecteur_size300_trimming.fasta

Tool : TargetP version 1.1 / Tmhmm version 2.0 / EffectorP  1.0 / SignalP 

Associated script : python_recup_index.py / script_secr.sh / trimming_size_prot_fasta.py / subset_fasta.py

Associated command line : script_secr.sh JN3.protein.fasta


Note : Terms used in the final 'annotation files' are descirbed as follow

SignalP	: Signal peptide prediction (SP = YES, none = NO)
TargetP	: localization prediction (TP = extracellular, none = other localization)
Tmhmm : transmembrane domain prediction (<=1 = 0 or 1 TM, >1 = more than 1 TM)
EffectorP : Prediction by EffectorP (effector or Non-effector)
EffectorP_prob : Accuracy of EffectorP prediction (probability from 0 to 1)
Repertoire_PPS : Predicted as SSP (criteria : SP or TP, <=1 TM, <300AA)
genes from mitochondrial genome were discarded from the SSP repertoire (10 protein)