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CanPredict specifications

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Unique identifier OMICS_00142
Name CanPredict
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

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Publications for CanPredict

CanPredict citations

 (10)
library_books

Practical aspects of NGS based pathways analysis for personalized cancer science and medicine

2016
Oncotarget
PMCID: 5239569
PMID: 27191992
DOI: 10.18632/oncotarget.9370

[…] located within functionally-related genes. observed significant differences suggest that the mutation under study may be involved in cancer development., several algorithms like chasm [] and canpredict [] treat the differentiation between driver and passenger somatic missense mutations as a classification problem. the random forest classifier is trained to distinguish between driver […]

library_books

Computational methods and resources for the interpretation of genomic variants in cancer

2015
BMC Genomics
PMCID: 4480958
PMID: 26111056
DOI: 10.1186/1471-2164-16-S8-S7

[…] trained on a subset of mutations with defined phenotypic effect. in particular, several methods have been developed for discriminating between passenger and cancer driver mutations [,-]. among them, canpredict [] has been the first algorithm for predicting cancer-causing mutations. the method uses a conservation measures from pfam [] hidden markov models and functional information encoded […]

library_books

Novel EPHB4 Receptor Tyrosine Kinase Mutations and Kinomic Pathway Analysis in Lung Cancer

2015
Sci Rep
PMCID: 4466581
PMID: 26073592
DOI: 10.1038/srep10641

[…] a abi prism 3730 dna analyzer (life technologies/applied biosystems, carlsbad ca) and has been fully established for use in testing clinical samples for the presence of cancer-associated mutations., canpredict was used to predict whether a non-synonymous variation would be deleterious to the structure and function of ephb4 using biochemical, evolutionary, and domain-function constraints. […]

library_books

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

2014
Int J Mol Sci
PMCID: 4100115
PMID: 24886813
DOI: 10.3390/ijms15069670

[…] [,], automute [,], fish [,], ond-crf [], prosms, protsrf, iptree-stab [], mupro, scide [,], scpred [], mustab [,], popmusic, pmut [,,], snap [], snps and gene ontology (snps&go) [], parepro [], canpredict [], nssnpanalyzer [,,], mutpred [], hansa [,], mutation taster [] and beatmusic []., besides studying the protein stability changes upon mutations, the sequence-based machine learning […]

library_books

Structure Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases

2014
PMCID: 4000980
PMID: 24817905
DOI: 10.1155/2014/653487

[…] suggests that cancer drivers have characteristics similar to mendelian disease mutations []. based on this information, a computational tool for predicting cancer-associated missense mutations, canpredict, was developed []. though quite powerful, generalized prediction methods such as canpredict may fail to achieve the sensitivity and specificity attainable by prediction models tailored […]

library_books

Assessment of computational methods for predicting the effects of missense mutations in human cancers

2013
BMC Genomics
PMCID: 3665581
PMID: 23819521
DOI: 10.1186/1471-2164-14-S3-S7

[…] change type in cosmic. notably the latter feature was ranked as second most predictive feature. chasm is available via the web application cravat (http://www.cravat.us)., analogously to condel, canpredict [] uses a random forest classifier to combine results from different methods. it uses sift and logre to determine the functional impact of changes, and gene ontology similarity score […]


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CanPredict institution(s)
Department of Bioinformatics, Genentech, Inc; South San Francisco, CA, USA

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