Table 3.
Bioinformatics tools and methods integrated into the Predector pipeline.
| Software | Description | References |
|---|---|---|
| (A) Localisation | ||
| SignalP v3.0, 4.1g, 5.0b | Extracellular secretion via signal peptide. Both NN and HMM methods are run for v3.0. Eukaryotic types specified | 23–25 |
| Deepsig commit 69e01cb | Extracellular secretion. *-k euk | 27 |
| Phobius 1.01 | Extracellular secretion | 26 |
| LOCALIZER v1.0.4 | Host sub-cellular localisation. Using predicted mature proteins from SignalP 5.0b. *-e -M | 34 |
| ApoplastP v1.0.1 | Apoplast-specific localisation | 35 |
| DeepLoc v1.0 | Sub-cellular localisation | 29 |
| TargetP v2.0 | Sub-cellular localisation. *-org non-pl | 28 |
| TMHMM v2.0c | Membrane localisation via transmembrane domains. *-d | 30 |
| (B) Effector-like properties | ||
| EffectorP v1.0, 2.0 | Probabilistic prediction of effector likelihood | 31,32 |
| EMBOSS: pepstats v6.5.7 | Amino acid properties and frequencies | 65 |
| (C) Functional annotation | ||
| HMMER (vs dbCAN v8) v3.2.1 | Used to search dbcan | 60,66 |
| MMSeqs2 v10-6d92c (vs PHIBase v4.9) | Used to search phibase. *--max-seqs 300 -e 0.01 -s 7 --num-iterations 3 -a | 40,55 |
| MMSeqs2 v10-6d92c (vs known effectors in Supplementary Table S2) | *--max-seqs 300 -e 0.01 -s 7 --num-iterations 3 -a | 55 |
| PfamScan (vs Pfam v33.1) | With active site prediction. *-as | 67 |
*Non-default parameters are indicated where applicable.