Condel protocols

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Condel specifications

Information


Unique identifier OMICS_00146
Name Condel
Alternative names CONsensus DELeteriousness score of missense SNVs, FannsDB web server
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Beta
Registration required Yes
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline Abel González-Pérez <>
  • person_outline Núria López-Bigas <>

Publication for CONsensus DELeteriousness score of missense SNVs

Condel in pipelines

 (3)
2016
PMCID: 5545709
PMID: 27404287
DOI: 10.1038/tp.2016.120

[…] was performed using bwa. gatk was used for variant calling and annovar for functional annotation. rare mutations predicted deleterious (loss of function or missense predicted damaging with the condel program) were selected. we also analyzed exome data of asd patients available from dbgap (accession=phs000482.v1.p1 and phs000298.v1.p1; n=931) in order to define the number of deleterious […]

2015
PMCID: 4319975
PMID: 25658757
DOI: 10.1371/journal.pone.0117418

[…] (developed by coco dong and dr. xiaoming liu, university of southern california, http://www.openbioinformatics.org/annovar/annovar_filter.html). complementary annotations were performed using condel v2.0 [], alamut v2.3 (interactive biosoftware) and ingenuity variant analysis (www.ingenuity.com/variants) softwares., the stil mutation c.2150g>a was confirmed in the mother i2 and the boy […]

2014
PMCID: 4094938
PMID: 24823478
DOI: 10.3390/genes5020366

[…] strelka [] and seurat [] which were used with their default settings. in addition, we used the intogen-mutations platform [,] to identify genes mutated in the tcga/iccg cancer genome projects. the condel online tool [] was used to obtain scores for missense mutations [] shown in the exome sequencing data tables. we also used the ingenuity variant analysis web-based application to compare […]


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Condel in publications

 (158)
PMCID: 5940219
PMID: 29738578
DOI: 10.1371/journal.pone.0196939

[…] to restrictions of some of the predictors. rdriver was able to achieve evidently better classification performance (auc = 0.85) on this set than other predictors (), followed by gerp (auc = 0.78), condel (auc = 0.75), sift, polyphen and a frequency based approach ()., encouraged by our results on the brca data, we further expanded rdriver analysis to a tcga pan-cancer cohort (), which included […]

PMCID: 5934427
PMID: 29755507
DOI: 10.3389/fgene.2018.00146

[…] ibd causative il10-ra mutations. the sensitivity and specificity analysis of different computational methods showed that cadd outperform sift, polyphen 2.0, fathmm, lrt, metalr, metasvm, provean and condel in predicting the pathogenicity of il10ra mutations. our three-dimensional protein modeling assays showed that the point mutations cause major drifts in the structural plasticity of il10 ra […]

PMCID: 5921983
PMID: 29719671
DOI: 10.1186/s13229-018-0205-9

[…] and gnomad. the missense mutation in s14 (p.asp1672tyr) affects a highly conserved residue and is predicted to be damaging by all algorithms used, including polyphen-2, sift, panther, mutpred2, condel2, cadd, and m-cap (additional file : table s3).table 1anm_033517.1bnp_277052.1 (q9byb0-1)cs1 also has a de novo pathogenic 17q12 microduplication []. reported previously [, , ]dreported […]

PMCID: 5902451
PMID: 29662108
DOI: 10.1038/s41598-018-24286-2

[…] score is larger, the more likely the sap will be deleterious., we combined these three normalized scores into a weighted average score, referred to as the ‘meta-score,’ using the previously published condel method.3\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} […]

PMCID: 5929434
PMID: 29731991
DOI: 10.18632/oncotarget.24924

[…] were identified, but mutations were infrequent. out of the 27 mutations detected in 7 samples, 8 (ctnnb1, mecom, znf536, egfr, eml4, csmd3, pbrm1, ppp1r3a) were identified as deleterious (on condel, polyphen and sift) and a truncating mutation was found in nf2. of these, egfr and nf2 are potential driver mutations and have not been reported previously in liposarcoma. mdm2 and cdk4 […]


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Condel institution(s)
Research Programme on Biomedical Informatics, Universitat Pompeu Fabra, Parc de Recerca Biomedica de Barcelona, Barcelona, Spain
Condel funding source(s)
Supported by the Spanish Ministerio de Educacion y Ciencia, grant number SAF2009-06954 and the Spanish National Institute of Bioinformatics (INB).

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