SecretomeP protocols

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SecretomeP specifications

Information


Unique identifier OMICS_03893
Name SecretomeP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Soren Bruk <>

Publication for SecretomeP

SecretomeP in pipelines

 (17)
2017
PMCID: 5209865
PMID: 28049427
DOI: 10.1186/s12864-016-3468-6

[…] regions, coiled coils and classical secretory sequences were gathered from the wormbase parasite biomart database for h. bacteriophora []. non-classical secretory peptides were found using secretomep v1.0f []. in order to better understand global gene ontology classifications, terms were condensed into higher functional categories using wego []. to determine if any go terms […]

2017
PMCID: 5361795
PMID: 28327085
DOI: 10.1186/s12866-017-0925-6

[…] the expressione software, refer to the differences between biological replicates., the proteins identified in 1002_ovis under both conditions were analyzed using the following prediction tools: secretomep 2.0 server, to predict proteins exported from non-classical systems (positive prediction score greater than to 0.5) [] and pips software, to predict proteins in the pathogenicity islands […]

2017
PMCID: 5361795
PMID: 28327085
DOI: 10.1186/s12866-017-0925-6

[…] [pacheco et al. [], silva et al. [], bidentified in an isolated of c. pseudotuberculosis from ovine lymph nodes [rees et al. [], the proteins identified in both conditions were analyzed by secretomep [] to assess whether these proteins could be exported by non-classical secretion systems. among the expressed differentially proteins 31% (37 proteins) were predicted as secreted […]

2017
PMCID: 5507320
PMID: 28644839
DOI: 10.1371/journal.pgen.1006857

[…] (ko) groups using wu-blastp (e < 1e-5). proteins with signal peptides and transmembrane topology were identified using the phobius web server [], and non-classical secretion was predicted using secretomep 1.0 []. cegma (v.2.4) [] was used to assess the completeness of the genome without excluding partial matches. mega6.06 [] was used to estimate maximum likelihood phylogenies (lg+g model)., […]

2017
PMCID: 5695823
PMID: 29155854
DOI: 10.1371/journal.pone.0188105

[…] sequence, did not traffic to the mitochondria, and lacked transmembrane regions. in parallel, to predict proteins secreted via the non-classical secretory pathway in the same dataset, we used secretomep v2.0 (http://www.cbs.dtu.dk/services/secretomep/) [] for feature-based analysis and identification of secreted proteins that do not contain an n-terminal signal sequence motif. results […]


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SecretomeP in publications

 (258)
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] signal and predicted subcellular localization as extracellular were classified as extracellular proteins secreted through a non-classical secretion pathway (branch c in fig. ). to our knowledge, secretomep, is the only prediction tool for non-classical secretion pathway, however, secretomep, is designed for bacteria and mammals and not for fungi. still fsd has employed secretomep, to predict […]

PMCID: 5907296
PMID: 29713252
DOI: 10.1186/s12014-018-9193-1

[…] was performed using the kegg database (http://www.genome.jp/kegg/). secretory protein prediction and functional annotation were performed using signalp 4.1 (http://www.cbs.dtu.dk/services/signalp/), secretomep 2.0 (http://www.cbs.dtu.dk/services/secretomep/), and tmhmm, server 2.0 (http://www.cbs.dtu.dk/services/tmhmm/). ingenuity pathway analysis (ipa) was used to conduct functional analysis […]

PMCID: 5911502
PMID: 29713316
DOI: 10.3389/fmicb.2018.00738

[…] () was used to predict biosynthesis of secondary metabolites. transmembrane helices in proteins were predicted with tmhmm. transporter protein specificity was predicted by tcdb (). signalp and secretomep were used to predict signal peptides and secreted proteins, respectively (; ). to predict the twin-arginine motif we utilized tatp server (). autotransporter proteins were predicted […]

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

[…] a transmembrane domains (tmhmm 2.0) (emanuelsson et al., ); (c) subcellular localization (wolfpsort and targetp 1.1) (emanuelsson et al., ; horton et al., ); and (d) non-classical protein secretion (secretomep 2.0) (bendtsen et al., ) (supplementary figure ). moreover, prediction of secretory proteins was based on bioinformatics tools and parameters reported by two different fungal secretome […]

PMCID: 5883313
PMID: 29614953
DOI: 10.1186/s12864-018-4627-8

[…] of signals due to peptides of the secreted proteins was predicted by signalp v.4.0 (http://www.cbs.dtu.dk/services?signalp/) []. additionally, secretome pv2.0 (http://www.cbs.dtu.dk/services/secretomep/) was used to define the proteins that were secreted by the non-classic pathway []., for cazy enzyme identification, the proteins in the secretome were screened with a library of hidden […]


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SecretomeP institution(s)
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark

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