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KD4v: comprehensible knowledge discovery system for missense variant

Tien-Dao Luu, Alin Rusu, Vincent Walter, Benjamin Linard, Laetitia Poidevin, Raymond Ripp, Luc Moulinier, Jean Muller, Wolfgang Raffelsberger, Nicolas Wicker, Odile Lecompte, Julie D. Thompson (+2 others)
2012 Nucleic Acids Research  
The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants.  ...  The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates.  ...  ACKNOWLEDGEMENTS The IGBMC common services and BIPS platforms are acknowledged for their assistance.  ... 
doi:10.1093/nar/gks474 pmid:22641855 pmcid:PMC3394327 fatcat:w3ri226mdbfsllra5tay3rsbfu

Knowledge Discovery in Variant Databases Using Inductive Logic Programming

Hoan Nguyen, Tien-Dao Luu, Olivier Poch, Julie D. Thompson
2013 Bioinformatics and Biology Insights  
We extracted background knowledge from MSV3d, a database of all human missense variants mapped to 3D protein structure.  ...  In this work, we describe the use of a recent knowledge discovery from database (KDD) approach using inductive logic programming (ILP) to automatically extract knowledge about human monogenic diseases.  ...  Acknowledgements The Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) services are acknowledged for assistance.  ... 
doi:10.4137/bbi.s11184 pmid:23589683 pmcid:PMC3615990 fatcat:tp7dx3s5ybdnrnptlkhwl6lula

Screening RB1 Gene in Algerian Patients and Predicting the Pathogenicity of Variations by In Silico Analysis

Amina Mama Boubkeur, Lotfi Louhibi, Meriem Abdi, Fatima Zohra Moghtit, Nacera Tabet Aoul, Rym Abderrahmane, Khadija Mahmoudi, Meriem Aberkane, Nadhira Saidi Mehtar
2017 Journal of Clinical & Experimental Ophthalmology  
Among these mutations, some were identified in germinal level for children with no family history of the disease.  ...  The spectrum of mutation included 2 missense mutations, 1 nonsense mutation, 1 deletion, 1 mutation affecting splice site and 2 polymorphisms.  ...  KD4v: Comprehensible system for Knowledge Discovery missense variant software "KD4v" (http://decrypthon.igbmc.fr/kd4v) predicts whether a mutation has a neutral or deleterious effect on a protein [16]  ... 
doi:10.4172/2155-9570.1000653 fatcat:72ddyzqkrbhr5ksbebfjvgmoby

Single amino acid polymorphism in aldehyde dehydrogenase gene superfamily

C. George Priya Doss
2015 Frontiers in Bioscience  
KD4V (Comprehensive knowledge Discovery System for Missense Variations) server tends to characterize and predict the phenotypic effects (deleterious or neutral) of missense variants (118).  ...  TD Luu, A Rusu, V Walter, B Linard, L Poideven, R Ripp, L Moulinier, J Muller, W Raffelsberger, N Wicker, O Lecompte, JD Thompson, O Poch, H Nguyen : KD4v: comprehensible knowledge discovery system for  ... 
doi:10.2741/4313 pmid:25553455 fatcat:5mbzzwfkz5h7bftn5so5qtaabq

In SilicoPrediction of the Effects of Mutations in the Human Mevalonate Kinase Gene: Towards a Predictive Framework for Mevalonate Kinase Deficiency

Claire Browne, David J. Timson
2015 Annals of Human Genetics  
. & Nguyen, H. (2012) KD4v: Comprehensible 42 Knowledge Discovery System for Missense Variant.  ...  size ch KD4V charge KD4V polarit KD4V hydrop KD4V modific KD4V numbe KD4V WT res SNP effect HIDS V377I -0.118 -0.58 4 (Decrease) 3 (Large decr 6 (neutral) 0.149 Tolerated -0.561 Neutral 0.331  ... 
doi:10.1111/ahg.12126 pmid:26420133 fatcat:3tlnwgcv7nfpnppx2qsjpityma

Correlation of SPECT imaging, biochemical parameters and mutation with systolic dysfunction

D. Alenizi, N.A. Kizilbash, O. Gill, A. Abukanna, S. Malik, A. Badawy
2013 Genetics and Molecular Research  
In silico tools such as SIFT, PolyPhen-2, KD4v, and Project HOPE were used 5965 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 12 (4): 5964-5977 (2013) Coronary artery disease: SPECT, biochemical  ...  The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server provides physico-chemical properties of the phenotype of missense mutations.  ...  These mutations are: nonsense mutation W23X, missense mutations W66G and W556S, and splice-site mutations 313+1G>A and 1846-1G>A (Hobbs et al., 1992) .  ... 
doi:10.4238/2013.november.26.6 pmid:24338390 fatcat:wortxudbkfdcbnubxoi5sx5t3u

Abstracts for the 39th Human Genetics Society of Australasia Annual Scientific Meeting Perth, Western Australia: August 8–11, 2015

2015 Twin Research and Human Genetics  
We present results of biochemical genetics testing in a 4-year-old female, admitted to hospital following complications of chemotherapy for ALL.  ...  IP address: 207.241.231.82, on 27 Jul 2018 at 05:43:43, subject to the Cambridge Core terms of use, available at Abstracts for the 39th HGSA Annual Scientific Meeting in serum is age dependent and gender  ...  The variant was predicted to be pathogenic by analysis of the sequence on the PolyPhen2, Align GVGD, SIFT, and MutationTaster programs, while KD4v predicted it to be benign.  ... 
doi:10.1017/thg.2015.45 fatcat:k75mzrayyvfubohupfxuz5v4je