Computational protocol: Candidate effector proteins of the necrotrophic apple canker pathogen Valsa mali can suppress BAX-induced PCD

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Protocol publication

[…] The secretome of V. mali was obtained from the sequenced genome in our previous study (). The Whole-Genome Shotgun project for V. mali has been deposited at DDBJ/EMBL/GenBank under the accession JUIY01000000. CEPs were defined as extracellular proteins with no known function (e-value > 1e–5). Cysteine content was calculated using the pepstats program from the EMBOSS package (http://emboss.bioinformatics.nl/). Markov clustering analysis was performed using tribe-MCL (). The known effector motifs RXLR (), [L/I]xAR (), YxSL[R/K] (), [R/K]VY[L/I]R (), and [Y/F/W]xC () were searched for using the fuzzpro program from the EMBOSS package. Nuclear localization signals (NLSs) were predicted with NLStradamus (). De novo motif search was performed using MEME (). […]

Pipeline specifications

Software tools EMBOSS, TRIBE-MCL, NLStradamus
Databases DDBJ
Applications Protein sequence analysis, Protein interaction analysis
Organisms Malus domestica
Diseases Kartagener Syndrome, Mycoses
Chemicals Cysteine