Table 2.

Bioinformatics tools used in a coherent pipeline to identify putative effectors of P. brassicae.

Bioinformatics tool	Description	Website	Reference
Trimmomatic	A fast, multithreaded command line tool that can be used to trim and crop Illumina data as well as to remove adapters.	http://www.usadellab.org/trimmomatic	[80]
STAR	An algorithm for aligning high-throughput long and short RNA-seq data to a reference genome.	http://code.google.com/p/rna-star	[81]
SignalP	Software that predicts signal peptide cleavage sites in proteins from eukaryotes and prokaryotes.	http://www.cbs.dtu.dk/services/SignalP	[82]
WoLF PSORT	An algorithm that predicts the subcellular localization sites of proteins based on their amino acid sequences. It makes predictions based on both known sorting signal motifs and some correlative sequence features such as amino acid content.	www.wolfpsort.org	[83]
TargetP	Tool that predicts subcellular location of eukaryotic proteins.	http://www.cbs.dtu.dk/services/TargetP	[84]