PROVEAN pipeline

PROVEAN specifications

Information


Unique identifier OMICS_01849
Name PROVEAN
Alternative name Protein Variation Effect Analyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


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Maintainer


  • person_outline Agnes Chan <>

Information


Unique identifier OMICS_01849
Name PROVEAN
Alternative name Protein Variation Effect Analyzer
Interface Web user interface
Restrictions to use None
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Agnes Chan <>

Publications for Protein Variation Effect Analyzer

PROVEAN IN pipelines

 (5)
2016
PMCID: 5070092
PMID: 27756226
DOI: 10.1186/s12864-016-3163-7

[…] obtained from ncbi (refseq release 70) [25, 26]. we excluded mrna models that did not have full-length protein coding sequences. non-synonymous substitutions were subsequently evaluated with provean to predict functional impacts on protein structure [27]. three missense mutations, r203c in xm_003448054.2 (lg6), e1235v in xm_003438386.2 (lg13) and g215a in xm_005466093.1 (lg22), […]

2016
PMCID: 5070092
PMID: 27756226
DOI: 10.1186/s12864-016-3163-7

[…] functional impacts on protein structure [27]. three missense mutations, r203c in xm_003448054.2 (lg6), e1235v in xm_003438386.2 (lg13) and g215a in xm_005466093.1 (lg22), were excluded from the provean analysis due to low quality gene annotations as defined by provean. missense mutations harboring provean scores less than the recommended threshold of −2.5 were considered deleterious., […]

2016
PMCID: 5070092
PMID: 27756226
DOI: 10.1186/s12864-016-3163-7

[…] r203c in xm_003448054.2 (lg6), e1235v in xm_003438386.2 (lg13) and g215a in xm_005466093.1 (lg22), were excluded from the provean analysis due to low quality gene annotations as defined by provean. missense mutations harboring provean scores less than the recommended threshold of −2.5 were considered deleterious., sex-patterned snps in s. melanotheron were compared to the sex-patterned […]

2016
PMCID: 5070092
PMID: 27756226
DOI: 10.1186/s12864-016-3163-7

[…] e1235v in xm_003438386.2 (lg13) and g215a in xm_005466093.1 (lg22), were excluded from the provean analysis due to low quality gene annotations as defined by provean. missense mutations harboring provean scores less than the recommended threshold of −2.5 were considered deleterious., sex-patterned snps in s. melanotheron were compared to the sex-patterned snps identified in o. niloticus, […]

2014
PMCID: 4200523
PMID: 25268989
DOI: 10.1038/ncomms6114

[…] we ran funcisnp with the following parameters: ±200 kb around each of the 25 tag snps and r2>0.1. to analyze the potential effects of correlated snps on protein coding, we employed snpeff and provean using suggested default parameters. for analysis of snps on transcription factor motifs, we employ a method developed by hazelett et al.58, we note that tcga has strict sample criteria. […]

PROVEAN institution(s)
The J Craig Venter Institute, Chinakville, MD, USA

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