Phobius protocols

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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 in pipelines

 (65)
2018
PMCID: 5753508
PMID: 29298673
DOI: 10.1186/s12864-017-4407-x

[…] of signal peptides and signal peptide cleavage sites using the signalp v4.0 program []. subsequently, all proteins with signal peptides were analyzed for the presence of transmembrane domains using phobius [] and tmhmm version 2.0 []. the set of proteins with putative transmembrane domains was removed from the dataset. remaining secreted proteins were then clustered in multiple enzymatic […]

2018
PMCID: 5808241
PMID: 29467727
DOI: 10.3389/fmicb.2018.00082

[…] of proteins were done using emboss needle (http://www.ebi.ac.uk/tools/psa/emboss_needle/) with gap and extension penalties of 10 and 0.5, respectively, and transmembrane predictions were done using phobius (http://phobius.sbc.su.se/)., blast similarities with known meopn-transferases (cj1421 and cj1422) from nctc11168 indicated that gene 06810 might be the sole meopn-transferase found […]

2018
PMCID: 5820362
PMID: 29503658
DOI: 10.3389/fpls.2018.00185

[…] trees were constructed with mega7.0 software () using the maximum likelihood method with 1000 bootstrap replicates. the prediction of membrane-spanning regions and orientation was performed using phobius software ()., the 5-week old tobacco plants (obtained as described in the section “plant material and growth conditions”) were grown for the next 4 days in the control medium, […]

2018
PMCID: 5826349
PMID: 29515563
DOI: 10.3389/fmicb.2018.00312

[…] table ). transcript abundances without significant variations (p-values higher than 0.03) are shown in supplementary table ., the transmembrane topology of the sco4117 gene was analyzed using the phobius software (http://phobius.sbc.su.se/). the sco4117 orthologs were obtained from the strepdb database (http://strepdb.streptomyces.org.uk/): sli_4349 (s. lividans), sav_3491 (s. avermitilis), […]

2018
PMCID: 5844311
PMID: 29326229
DOI: 10.1534/g3.117.300421

[…] kaas (bidirectional best hit) (). putative secreted proteins were identified using signalp 4.1 () and wolf psort 0.2 (). secreted proteins were assessed for the presence of transmembrane helices by phobius () and thmmh 2.0 (). cyps were predicted as described elsewhere (). cyp proteins that could not be assigned to families or subfamilies based on the international p450 nomenclature committee […]


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Phobius in publications

 (518)
PMCID: 5940819
PMID: 29740007
DOI: 10.1038/s41598-018-24999-4

[…] 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 […]

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

[…] 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 […]

PMCID: 5938622
PMID: 29765384
DOI: 10.3389/fpls.2018.00546

[…] 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%), […]

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

[…] 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). […]

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

[…] (). 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 [] […]


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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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