PMut protocols

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PMut specifications

Information


Unique identifier OMICS_00159
Name PMut
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Beta
Maintained Yes

Maintainers


  • person_outline Josep Ll. Gelpí <>
  • person_outline Modesto Orozco <>
  • person_outline PMut Team <>

Additional information


http://mmb.pcb.ub.es/PMut/help http://mmb.pcb.ub.es/pmut2017/PyMut-tutorial

Information


Unique identifier OMICS_00159
Name PMut
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, Shell (Bash)
License MIT License
Computer skills Advanced
Version 0.1.1
Stability Stable
Requirements
anaconda
Maintained Yes

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Maintainers


  • person_outline Josep Ll. Gelpí <>
  • person_outline Modesto Orozco <>
  • person_outline PMut Team <>

Additional information


http://mmb.pcb.ub.es/PMut/help http://mmb.pcb.ub.es/pmut2017/PyMut-tutorial

Publications for PMut

PMut in pipeline

2013
PMCID: 3775809
PMID: 24069280
DOI: 10.1371/journal.pone.0074203

[…] resulted in two bands of 271 and 401 bp (primer sequences provided upon request). protein sequences were aligned with clustalw2 (http://www.ebi.ac.uk/tools/clustalw2/index.html). bioinformatic tools pmut [], panther version 7 [] and polyphen-2 [] were used to predict the impact of rare amino acid exchanges on protein structure and function., human calhm1 cdna was obtained from origene (maryland, […]


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PMut in publications

 (23)
PMCID: 5432510
PMID: 28507310
DOI: 10.1038/s41598-017-02074-8

[…] (http://evs.gs.washington.edu/evs/), exac (http://exac.broadinstitute.org/), and csvs (http://csvs.babelomics.org/). missense variations were analyzed in silico with different tools (polyphen-2, pmut, sift and mutation taster) to predict their pathogenicity and the impact on the disease. likewise, all variations were analyzed in silico to know if these missense, synonymous and nonsense […]

PMCID: 5399085
PMID: 28484394
DOI: 10.3389/fphys.2017.00231

[…] and comparative considerations (adzhubei et al., ). the generated protein function prediction score (humdiv) was scaled into either benign, possibly damaging or probably damaging. we also used the pmut (http://mmb2.pcb.ub.es:8080/pmut/), a web based server that could retrieve information from database of mutation hotspots, utilizes neural network to analyze the single nucleotide polymorphisms […]

PMCID: 5303298
PMID: 28187756
DOI: 10.1186/s12881-017-0377-8

[…] mutations were analysed for their pathogenic potential by using polyphen-2 version 2.2.2 [] http://genetics.bwh.harvard.edu/pph2/, sift blink [] http://sift.jcvi.org/www/sift_blink_submit.html, pmut [, ] http://mmb2.pcb.ub.es/pmut/ and snap [] http://rostlab.org/services/snap/ algorithms. pathogenicity classes were ascertained according to the guidelines suggested by wallis et al. 2013 […]

PMCID: 5024326
PMID: 27630060
DOI: 10.1038/srep33570

[…] software to align sequences and compare them with different organisms. rare missense variants were analyzed to predict their potential pathogenicity, used combined computer algorithms: polyphen-2, pmut, sort intolerant from tolerant (sift) and mutationtaster2 software. other combined computer algorithms were used to predict whether that change could affect donor/acceptor splice sites: hsf […]

PMCID: 4893224
PMID: 27260700
DOI: 10.1186/s12863-016-0384-3

[…] search tool (blast) software. polyphen-2 (available at http://genetics.bwh.harvard.edu/pph/) characterize an amino acid substitution as “benign”, “possibly damaging” or “probably damaging” [], pmut (available at http://mmb2.pcb.ub.es:8080/pmut/) provides a binary prediction of “neutral” or “pathologic” [], sort intolerant from tolerant (sift) (available at http://sift.jcvi.org) predict […]


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PMut institution(s)
Barcelona Supercomputing Center (BSC), Barcelona, Spain; Joint Program BSC-CRG-IRB Research Program for Computational Biology, Barcelona, Spain; Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain; Vall d’Hebron Institute of Research (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain; ICREA, Barcelona, Spain; Dept. of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
PMut funding source(s)
Spanish Ministry of Science [BIO2015-64802-R-32868, SEV-2015-0493, TIN2012-34557, TEC2015-67774-C2-2-R, SAF2016-80255-R], Catalan Government [2014-SGR-134,2014-SGR-1051], Instituto de Salud Carlos III-Instituto Nacional de Bioinformatica [INB; PT13/0001/0019, PT13/0001/0028], European Union, H2020 programme [Elixir-Excelerate: 676559; BioExcel: 674728 and MuG:676566] and La Caixa Foundation fellowship.

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