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Phobius specifications

Information


Unique identifier OMICS_03888
Name Phobius
Interface Web user interface
Restrictions to use None
Parallelization CUDA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Additional information


A standalone version is available for academic users only, on request.

Information


Unique identifier OMICS_03888
Name Phobius
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Protein sequence
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Medium
Version 1.01
Stability Stable
Requirements
Perl

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Documentation


Additional information


A standalone version is available for academic users only, on request.

Publications for Phobius

Phobius citations

 (538)
library_books

A Meloidogyne incognita effector MiISE5 suppresses programmed cell death to promote parasitism in host plant

2018
Sci Rep
PMCID: 5940819
PMID: 29740007
DOI: 10.1038/s41598-018-24999-4

[…] pt M. javanica were download from NCBI (Table ). The predictions of the signal peptide were performed using SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP/), predisi (http://www.predisi.de/) and phobius (http://phobius.binf.ku.dk/). The prediction of transmembrane and conserved domain were performed using TMHMM (http://www.cbs.dtu.dk/services/TMHMM-2.0/) and NCBI CD-Search (https://www.ncbi.n […]

library_books

Systematic mapping of contact sites reveals tethers and a function for the peroxisome mitochondria contact

2018
Nat Commun
PMCID: 5932058
PMID: 29720625
DOI: 10.1038/s41467-018-03957-8

[…] zation information was obtained from the literature as well as from the C′ GFP library. (2) Having the tagged termini facing the cytosol. The orientation was obtained from the literature as well from Phobius transmembrane topology tool (http://phobius.sbc.su.se/),. (3) Expressed at high abundance. Protein abundance (molecules per cell) information was obtained from ref. . We chose for tagging 26 c […]

library_books

The Hydrophobin Like OmSSP1 May Be an Effector in the Ericoid Mycorrhizal Symbiosis

2018
Front Plant Sci
PMCID: 5938622
PMID: 29765384
DOI: 10.3389/fpls.2018.00546

[…] further analyses, with a preference for those uniquely or highly expressed in symbiosis that did not contain PFAM motifs with known functions (Table ). Three different software (PrediSi, SIgnalP 4.1, Phobius) confirmed the presence of a signal peptide (Table ), but alignment of the primary sequences indicated very low similarities. Cysteine enrichment > 3% was only observed for OmSSP1 (8.6%), the […]

library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] o predict protein-based features in our secretome prediction pipeline. The presence of a signal peptide in the N-terminus was predicted using SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP/) and Phobius (http://phobius.sbc.su.se/). The presence of GPI anchor was predicted using PredGPI (http://gpcr.biocomp.unibo.it/predgpi/) and big-PI (http://mendel.imp.ac.at/gpi/fungi_server.html). The pres […]

library_books

Evolutionary novelty in gravity sensing through horizontal gene transfer and high order protein assembly

2018
PLoS Biol
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] ee (). All other species trees (, and Figs) were constructed from 400 conserved protein sequences by PhyloPhlAn using RefSeq bacterial proteomes. The presence of signal sequence was predicted using Phobius []. Phylogenetic trees were visualized with ETE3 [].To construct OCTIN protein trees (Figs and and ), OCTIN sequences from the NCBI reference protein database were used. MAFFT [] with the op […]

library_books

Forward Genetic Dissection of Biofilm Development by Fusobacterium nucleatum: Novel Functions of Cell Division Proteins FtsX and EnvC

2018
MBio
PMCID: 5915739
PMID: 29691334
DOI: 10.1128/mBio.00360-18

[…] ll division in fusobacteria and that in the absence of ftsX or envC, the cell envelope is visibly altered, lacking the microfolds that characterize the wild-type cells.By domain analysis using TMHMM, Phobius, and CCTOP programs (), F. nucleatum FtsX was predicted to have four transmembrane (TM) domains with three cytoplasmic regions and two extracellular domains (ECD) similar to the E. coli counte […]

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Phobius institution(s)
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden; Department of Molecular Biology, University of Copenhagen, Copenhagen, Denmark

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