AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations
作者： Hue Vuong , Robert M. Stephens , Natalia Volfovsky
DOI: 10.1093/BIOINFORMATICS/BTT655
关键词: Data mining 、 The Internet 、 Information retrieval 、 Visualization 、 Web server 、 Genomics 、 Thesaurus (information retrieval) 、 Genome 、 Context (language use) 、 Biology 、 Annotation
摘要: Motivation: The plethora of information that emerges from large-scale genome characterization studies has triggered the development computational frameworks and tools for efficient analysis, interpretation visualization genomic data. Functional annotation variations ability to visualize data in context whole and/or multiple genomes remained a challenging task. We have developed an interactive web-based tool, AVIA (Annotation, Visualization Impact Analysis), explore interpret large sets (single nucleotide insertion/deletions) help guide summarize experiments. The annotation, summary plots tables are packaged can be downloaded by user email link provided. Availability implementation: http://avia.abcc.ncifcrf.gov. Contact: vog.hin.liam@mhgnouv Supplementary information: Supplementary available at Bioinformatics online.
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S.A. Forbes, G. Bhamra, S. Bamford, E. Dawson, C. Kok, J. Clements, A. Menzies, J.W. Teague, P.A. Futreal, M.R. Stratton, The Catalogue of Somatic Mutations in Cancer (COSMIC). Current protocols in human genetics. ,vol. 57, ,(2008) , 10.1002/0471142905.HG1011S57
Ivan Adzhubei, Daniel M. Jordan, Shamil R. Sunyaev, Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 Current protocols in human genetics. ,vol. 76, ,(2013) , 10.1002/0471142905.HG0720S76
Florian Gnad, Albion Baucom, Kiran Mukhyala, Gerard Manning, Zemin Zhang, Assessment of computational methods for predicting the effects of missense mutations in human cancers BMC Genomics. ,vol. 14, pp. 1- 13 ,(2013) , 10.1186/1471-2164-14-S3-S7
Prateek Kumar, Steven Henikoff, Pauline C Ng, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols. ,vol. 4, pp. 1073- 1081 ,(2009) , 10.1038/NPROT.2009.86
K. Wang, M. Li, H. Hakonarson, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Research. ,vol. 38, ,(2010) , 10.1093/NAR/GKQ603
M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets Nucleic Acids Research. ,vol. 40, pp. 109- 114 ,(2012) , 10.1093/NAR/GKR988
I. Medina, A. De Maria, M. Bleda, F. Salavert, R. Alonso, C. Y. Gonzalez, J. Dopazo, VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing Nucleic Acids Research. ,vol. 40, pp. 54- 58 ,(2012) , 10.1093/NAR/GKS572
KONRAD J. KARCZEWSKI, ROBERT P. TIRRELL, PABLO CORDERO, NICHOLAS P. TATONETTI, JOEL T. DUDLEY, KEYAN SALARI, MICHAEL SNYDER, RUSS B. ALTMAN, STUART K. KIM, Interpretome: a freely available, modular, and secure personal genome interpretation engine. pacific symposium on biocomputing. pp. 339- 350 ,(2011) , 10.1142/9789814366496_0033
Xiaoming Liu, Xueqiu Jian, Eric Boerwinkle, dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations Human Mutation. ,vol. 34, ,(2013) , 10.1002/HUMU.22376
Jian Ren, Chunhui Jiang, Xinjiao Gao, Zexian Liu, Zineng Yuan, Changjiang Jin, Longping Wen, Zhaolei Zhang, Yu Xue, Xuebiao Yao, PhosSNP for Systematic Analysis of Genetic Polymorphisms That Influence Protein Phosphorylation Molecular & Cellular Proteomics. ,vol. 9, pp. 623- 634 ,(2010) , 10.1074/MCP.M900273-MCP200