EffectorP protocols

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EffectorP specifications

Information


Unique identifier OMICS_14236
Name EffectorP
Interface Web user interface
Restrictions to use None
Input data A protein sequence or several protein sequences.
Input format FASTA
Output data A summary table which shows the predictions (effector or non-effector) for each submitted protein.
Output format FASTA
Programming languages Python
License GNU General Public License version 3.0
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jana Sperschneider <>

Information


Unique identifier OMICS_14236
Name EffectorP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
EMBOSS, WEKA
Maintained Yes

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Maintainer


  • person_outline Jana Sperschneider <>

Publications for EffectorP

EffectorP in pipelines

 (5)
2018
PMCID: 5815587
PMID: 29451893
DOI: 10.1371/journal.pone.0191824

[…] as the pacbio assembly, with 2.67–5.25% of these assemblies masked. a total of 9925–10330 genes were predicted in these assemblies ()., putative secreted effector proteins were identified using effectorp and through searches for sscps. results of effector prediction were broadly similar between the five sequenced isolates, with 186–196 effectorp candidates and 125–136 sscps (). this led […]

2017
PMCID: 5256205
PMID: 28082505
DOI: 10.1128/genomeA.01479-16

[…] in a reduced cohort of gene predictions (n = 870), much more in line with those recently identified in other fungal pathogens species, of which 97 are predicted to be gpi-anchored. we also used effectorp to predict a sub-set of secreted effector proteins (n = 183), and updated the gene models with 5,694 5′ and 5,036 3′ untranslated region (utr) annotations., the f. graminearum strain ph-1 […]

2017
PMCID: 5381539
PMID: 28204478
DOI: 10.1093/gbe/evx030

[…] contained transmembrane domains, 3) gpisom (available at http://gpi.unibe.ch/) () was used to filter out proteins that harbored a putative glycophosphatidylinositol membrane-anchoring domain, and 4) effectorp version 1.0 () was used to predict potential effector sequences among those remaining after the previous filtering steps., a subset of the rnaseq data, data set 1, that were used for gene […]

2017
PMCID: 5381539
PMID: 28204478
DOI: 10.1093/gbe/evx030

[…] prediction in the version two annotations” above but used pfam instead of gpi-som to predict gpi-anchoring domains. to identify a subset of the secreted proteins that were potential effectors, effectorp was run. the whole pipeline for secreted protein discovery is available at: https://github.com/markcharder/generalbioinformaticsscripts/blob/master/effector_pipeline.sh. repeats […]

2017
PMCID: 5573122
PMID: 28846714
DOI: 10.1371/journal.pone.0183567

[…] signal and gpi anchors, respectively. the secretory proteins with nuclear localization signal were identified using nlstradamus (v1.8) [], while putative effector proteins were predicted through effectorp (v1.0) []. carbohydrate active enzymes (cazymes) were identified by hmmer (v3.1b1, http://hmmer.janelia.org/) scan against the family-specific hmm profiles of dbcan release 2.0 []. putative […]


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EffectorP in publications

 (25)
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] the secretomes of aspergillus species to enable discovery of potential virulence proteins (supplementary table ). note that effector-like proteins of aspergillus species were predicted based on effectorp predictions or cysteine content of ssps (methods). we found that ssps and effector-like proteins account for more than 30% and 10%, respectively, of the secretomes in aspergillus species […]

PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] 1568, 1868 and 1661 predicted genes for m4, 11,137 and dw5 respectively (table ).table 2agenbank version 1.0, bno. of genes with rna-seq support (100%). cno. of genes with effector prediction (effectorp score >= 0.5). dno. genes with proteogenomics support overlap on same strand. erna-seq data pooled. fbenchmarking universal single-copy orthologs (busco), agenbank version 1.0, bno. […]

PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] are described as fungal effectors []. the f. venenatum and f. graminearum secretomes were predicted using an identical pipeline [], whilst the candidate effector repertoire was predicted using effectorp []. within both fusaria, the secretome and putative effectors encoding genes were found to localise to chromosomal regions of low nucleotide homology (fig. ). a sequence homology analysis […]

PMCID: 5907361
PMID: 29669603
DOI: 10.1186/s12915-018-0508-5

[…] and 86% (138/160, additional file : st1i) coded for small proteins (fig. ). interestingly, 59% of these small proteins were predicted to be putative effectors from a. euteiches or a. astaci using effectorp (additional file : st1i), a software based on properties shared by fungal effectors []. this suggests that aphanomyces species presented a set of ssps similar to fungal effectors.fig. 3, […]

PMCID: 5896443
PMID: 29675028
DOI: 10.3389/fpls.2018.00409

[…] secretome databases: fungal secretome database (fsd) (choi et al., ) and funseckb2 (meinken et al., ), and one plant secretome database: planseckb (min et al., ). additionally, the prediction tool effectorp was used to identify putative effectors-like proteins from t. virens (sperschneider et al., ). predicted functional analysis of the aps was performed using blast2go that combines go […]


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EffectorP institution(s)
Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia; Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia; CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, Australia; Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
EffectorP funding source(s)
Supported by a CSIRO OCE Postdoctoral Fellowship.

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