Philius protocols

View Philius computational protocol

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Philius specifications

Information


Unique identifier OMICS_03887
Name Philius
Interface Web user interface, Application programming interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Michael Riffle <>

Additional information


Web app: http://www.yeastrc.org/philius/pages/philius/runPhilius.jsp Web service: http://www.yeastrc.org/philius/pages/philius/philius_webservices_info.jsp

Information


Unique identifier OMICS_03887
Name Philius
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Source code URL https://noble.gs.washington.edu/proj/philius/python/
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Michael Riffle <>

Additional information


Web app: http://www.yeastrc.org/philius/pages/philius/runPhilius.jsp Web service: http://www.yeastrc.org/philius/pages/philius/philius_webservices_info.jsp

Publication for Philius

Philius in pipelines

 (4)
2016
PMCID: 4877106
PMID: 27213534
DOI: 10.1371/journal.pone.0156015

[…] and ers1026453, respectively, in study number prjeb12251., standard programs used to analyse the sequences included the emboss [], expasy [] and ncbi suites [], as well as signalp 4.1 [] and philius []. the locations of orfs encoding functional proteins were predicted initially by identifying all atg-initiated orfs larger than 50 codons. orfs overlapping larger orfs for more than half […]

2016
PMCID: 5015957
PMID: 27606673
DOI: 10.1371/journal.pntd.0004988

[…] the above bioinformatic pipeline were further analyzed using the following eight prediction tools. cello version 2.5 (http://cello.life.nctu.edu.tw/) [] was used to predict subcellular localization. philius (http://www.yeastrc.org/philius/pages/philius/runphilius.jsp) [], phobius (http://phobius.sbc.su.se/) [], octopus/spoctopus (http://octopus.cbr.su.se/index.php) [], hmmtop version 2.0 […]

2016
PMCID: 5015957
PMID: 27606673
DOI: 10.1371/journal.pntd.0004988

[…] []. proteins with unclear subcellular localization predictions using the above bioinformatics pipeline (n = 25) were further analyzed using an additional eight prediction tools including cello [], philius [], phobius [], octopus/spoctopus [], hmmtop [], tmpred, bomp [] and tmbetadisc-rbf []. a results summary of this analysis can be found in and ., in total, 116 proteins were designated […]

2015
PMCID: 4486849
PMID: 26191053
DOI: 10.3389/fmicb.2015.00661

[…] programs: (1) signalip 4.1 (petersen et al., ) was used for gram-negative bacteria sequences; (2) pred-signal (bagos et al., ) was used for an archaeal sequence (methanohalobium evestigatum) ; (3) philius (reynolds et al., ) was used for the prediction of the presence of a secretion signal and protein type., gene of the recombinant dnase from thioalkalivibrio sp. k90mix (dnaseta) was de novo […]


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Philius in publications

 (18)
PMCID: 5875014
PMID: 29598818
DOI: 10.1186/s12934-018-0901-3

[…] that are either based on weight matrices, sequence alignments, neural networks, or machine learning algorithms, respectively []. for sec signal peptides, phobius (http://phobius.sbc.su.se/ []), philius (http://www.yeastrc.org/philius/pages/philius/runphilius.jsp []), and signalp (current version 4.1; http://www.cbs.dtu.dk/services/signalp []) are among the top scoring and most popular […]

PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] with putative dnase activity, []. besides the rhsa domain and the rhs repeat-associated core, we detected 3 transmembrane helices in the n-terminal region of this rhs-family protein with the philius transmembrane prediction tool (http://www.yeastrc.org/philius/runphilius.do) and it was also detected with the tmhmm tool as one of the svbp6 genome features with a transmembrane portion (). […]

PMCID: 5725453
PMID: 29230036
DOI: 10.1038/s41598-017-17621-6

[…] 3a viral protein. the 3a protein is myristoylated at the n-terminal glycine residue and also contains a hydrophobic region that every algorithm tested (cctop, hmmtop, membrain, memsat, octopus, philius, phobius, pro, prodiv, scampi, scampimsa, and tmhmm) predicts as a transmembrane helix that could anchor 3a protein in the lipid bilayer (fig.  upper panel). this is also supported […]

PMCID: 5412288
PMID: 28346351
DOI: 10.3390/ijms18040702

[…] phosphatase were used (1:30,000; sigma-aldrich)., predictions of chs3 topology were done with tmpred [], polyview [], phobius [], das tm filter [], hmmtop [], tmhmm 2.0 [], tmhmm 1.0 [], and philius []. homology-based 3d structure predictions were made with phyre2 [] and raptorx []. visualization of 3d structural models was performed with pymolv1.3., although chs3 has been extensively […]

PMCID: 5167687
PMID: 28066334
DOI: 10.3389/fmicb.2016.01989

[…] prokaryotes (). many methods have been used for predicting signal peptides, including signalp (; ; ; ), predisi (), speplip (), signal-cf (), signal-3l (), signal-blast (), phobius (), lipop () and philius (). all the prediction methods have limited ability to discriminate between signal peptides and n-terminal transmembrane helices. the common characteristic of signal peptides and n-terminal […]


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Philius institution(s)
Department of Electrical Engineering, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Biochemistry, University of Washington, Seattle, WA, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
Philius funding source(s)
Supported by National Institutes of Health (NIH) awards R01-EB007057 and P41-RR11823 and by an NIH National Research Service Award Training Grant.

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