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ProtFun specifications

Information


Unique identifier OMICS_17955
Name ProtFun
Interface Web user interface
Restrictions to use None
Input data A genome sequence.
Input format FASTA
Computer skills Basic
Version 2.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline L. Jensen

Publication for ProtFun

ProtFun citations

 (44)
library_books

Genome wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.)

2018
PLoS One
PMCID: 5764346
PMID: 29324804
DOI: 10.1371/journal.pone.0191081

[…] To predict the cellular and/or biological roles of SacEXP, GO category annotation was analyzed by employing the ProtFun server. In SacEXPs, with exception of SacEXP29, included in transport and binding category, all others SacEXPs were classified into the cell envelope functional category. The most enriched GO […]

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Immunomodulatory Effects of Amblyomma variegatum Saliva on Bovine Cells: Characterization of Cellular Responses and Identification of Molecular Determinants

2018
PMCID: 5759025
PMID: 29354598
DOI: 10.3389/fcimb.2017.00521
call_split See protocol

[…] We used several web servers to investigate the biochemical properties of the identified proteins.The ProtFun 2.2 server produces ab initio predictions of protein function from sequences. The method queries a large number of other feature prediction servers to obtain information on various post-transl […]

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A database for orphan genes in Poaceae

2017
PMCID: 5615222
PMID: 28966675
DOI: 10.3892/etm.2017.4918
call_split See protocol

[…] he isoelectric points (PI) and molecular weights (Mw) were retrieved from Expasy (http://www.expasy.org/) (). Function prediction based on the cellular role and Gene Ontology (GO) were collected from Protfun (http://www.cbs.dtu.dk/services/ProtFun/) (). WOLF PSORT (http://www.genscript.com/psort/wolf_psort.html) () was used for the prediction of subcellular localization. […]

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The Membrane Protein LasM Promotes the Culturability of Legionella pneumophila in Water

2016
PMCID: 5039212
PMID: 27734007
DOI: 10.3389/fcimb.2016.00113
call_split See protocol

[…] s used to predict transmembrane helices (Sonnhammer et al., ; Krogh et al., ). Second, SignalP 4.1 Server was used to predict the presence and location of signal peptides (Petersen et al., ). Lastly, ProtFun 2.2 Server was used to predict cellular role, enzyme class as well as the gene ontology category based on the amino acid sequence (Jensen et al., , ). […]

library_books

ProtNN: fast and accurate protein 3D structure classification in structural and topological space

2016
BioData Min
PMCID: 5034655
PMID: 27688811
DOI: 10.1186/s13040-016-0108-2

[…] assigned with the same class of the most similar (based on the sequence or the structure) reference protein. There exists several classification methods based on the protein sequence (e.g. Blast [], ProtFun [], SVM-Prot [, ] …); or on the protein structure (e.g. Combinatorial Extension [], Sheba [], FatCat [], Fragbag [], …). These methods rely on the assumption that proteins sharing the most com […]

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Characterization of a Novel Endoplasmic Reticulum Protein Involved in Tubercidin Resistance in Leishmania major

2016
PLoS Negl Trop Dis
PMCID: 5015992
PMID: 27606425
DOI: 10.1371/journal.pntd.0004972
call_split See protocol

[…] iction of transmembrane domains was performed with the TMHMM Server [, ] while the predictions of protein function, sub-cellular localization and the tridimensional TRP structure were performed using ProtFun [, ], TargetP Server [, ] and Phyre2 [], respectively.The sequence data described in this paper are available under the following accession numbers: XM_001685128.1 for gene ID LmjF.31.1940 (nu […]

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ProtFun institution(s)
Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark, Lyngby, Denmark
ProtFun funding source(s)
Supported by grants from the Danish National Research Foundation and the Danish Natural Science Research Council.

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