A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
作者： Pablo Cingolani , Adrian Platts , Le Lily Wang , Melissa Coon , Tung Nguyen
DOI: 10.4161/FLY.19695
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摘要: We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once is sequenced, SnpEff annotates based on their genomic locations and predicts coding effects. Annotated include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding such as synonymous non-synonymous amino acid replacement, start codon gains losses, stop frame shifts can be predicted. Here use illustrated by annotating ~356,660 candidate SNPs ~117 Mb unique sequences, representing substitution rate ~1/305 nucleotides, between Drosophila melanogaster w1118; iso-2; iso-3 strain reference y1; cn1 bw1 sp1 strain. show that ~15,842 are ~4,467 (N/S ~0.28). The remaining other categories, (38 SNPs), losses (8 (297 SNPs) in...
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E. Schadt, First Steps on a Long Road Science. ,vol. 331, pp. 691- 691 ,(2011) , 10.1126/SCIENCE.1203235
David Gatfield, Leonie Unterholzner, Francesca D Ciccarelli, Peer Bork, Elisa Izaurralde, Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways The EMBO Journal. ,vol. 22, pp. 3960- 3970 ,(2003) , 10.1093/EMBOJ/CDG371
Venkateswara R Chintapalli, Jing Wang, Julian A T Dow, Using FlyAtlas to identify better Drosophila melanogaster models of human disease Nature Genetics. ,vol. 39, pp. 715- 720 ,(2007) , 10.1038/NG2049
J. C. Chang, Y. W. Kan, beta 0 thalassemia, a nonsense mutation in man Proceedings of the National Academy of Sciences of the United States of America. ,vol. 76, pp. 2886- 2889 ,(1979) , 10.1073/PNAS.76.6.2886
William Saurin, Maurice Hofnung, Elie Dassa, Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters. Journal of Molecular Evolution. ,vol. 48, pp. 22- 41 ,(1999) , 10.1007/PL00006442
S. BRENNER, A. O. W. STRETTON, S. KAPLAN, Genetic Code: The ‘Nonsense’ Triplets for Chain Termination and their Suppression Nature. ,vol. 206, pp. 994- 998 ,(1965) , 10.1038/206994A0
B. Charlesworth, J. A. Coyne, N. H. Barton, The Relative Rates of Evolution of Sex Chromosomes and Autosomes The American Naturalist. ,vol. 130, pp. 113- 146 ,(1987) , 10.1086/284701
Van Khanh Tran, Yasuhiro Takeshima, Zhujun Zhang, Yasuaki Habara, Kazuhiro Haginoya, Atsushi Nishiyama, Mariko Yagi, Masafumi Matsuo, A nonsense mutation-created intraexonic splice site is active in the lymphocytes, but not in the skeletal muscle of a DMD patient Human Genetics. ,vol. 120, pp. 737- 742 ,(2006) , 10.1007/S00439-006-0241-Y
Douglas M. Ruden, D. Curtis Jamison, Barry R. Zeeberg, Mark D. Garfinkel, John N. Weinstein, Parsa Rasouli, Xiangyi Lu, The EDGE Hypothesis: Epigenetically Directed Genetic Errors in Repeat-Containing Proteins (RCPs) Involved in Evolution, Neuroendocrine Signaling, and Cancer Frontiers in Neuroendocrinology. ,vol. 29, pp. 428- 444 ,(2008) , 10.1016/J.YFRNE.2007.12.004
Kevin M. Flanigan, Diane M. Dunn, Andrew von Niederhausern, Michael T. Howard, Jerry Mendell, Anne Connolly, Carol Saunders, Ann Modrcin, Majed Dasouki, Giacomo P. Comi, Roberto Del Bo, Angela Pickart, Richard Jacobson, Richard Finkel, Livija Medne, Robert B. Weiss, DMD Trp3X nonsense mutation associated with a founder effect in North American families with mild Becker muscular dystrophy Neuromuscular Disorders. ,vol. 19, pp. 743- 748 ,(2009) , 10.1016/J.NMD.2009.08.010