An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.
作者： Diogo Pratas , Raquel M. Silva , Armando J. Pinho , Paulo J.S.G. Ferreira
DOI: 10.1038/SREP10203
关键词:
摘要: Species evolution is indirectly registered in their genomic structure. The emergence and advances sequencing technology provided a way to access genome information, namely identify study evolutionary macro-events, as well chromosome alterations for clinical purposes. This paper describes completely alignment-free computational method, based on blind unsupervised approach, detect large-scale small-scale rearrangements between pairs of DNA sequences. To illustrate the power usefulness method we give complete chromosomal information maps human-chimpanzee human-orangutan. tool by means which these results were obtained has been made publicly available described detail.
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sci-hub.se 参考文章(66)
I. Cusco, R. Corominas, M. Bayes, R. Flores, N. Rivera-Brugues, V. Campuzano, L. A. Perez-Jurado, Copy number variation at the 7q11.23 segmental duplications is a susceptibility factor for the Williams-Beuren syndrome deletion Genome Research. ,vol. 18, pp. 683- 694 ,(2008) , 10.1101/GR.073197.107
Giovanni Manzini, Marcella Rastero, A simple and fast DNA compressor Software - Practice and Experience. ,vol. 34, pp. 1397- 1411 ,(2004) , 10.1002/SPE.619
M. Brudno, S. Malde, A. Poliakov, C. B. Do, O. Couronne, I. Dubchak, S. Batzoglou, Glocal alignment: finding rearrangements during alignment Bioinformatics. ,vol. 19, pp. 54- 62 ,(2003) , 10.1093/BIOINFORMATICS/BTG1005
Adam Siepel, Gill Bejerano, Jakob S Pedersen, Angie S Hinrichs, Minmei Hou, Kate Rosenbloom, Hiram Clawson, John Spieth, LaDeana W Hillier, Stephen Richards, George M Weinstock, Richard K Wilson, Richard A Gibbs, W James Kent, Webb Miller, David Haussler, Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Research. ,vol. 15, pp. 1034- 1050 ,(2005) , 10.1101/GR.3715005
S. Grumbach, F. Tahi, Compression of DNA sequences data compression conference. pp. 340- 350 ,(1993) , 10.1109/DCC.1993.253115
X. Chen, M. Li, B. Ma, J. Tromp, DNACompress: fast and effective DNA sequence compression. Bioinformatics. ,vol. 18, pp. 1696- 1698 ,(2002) , 10.1093/BIOINFORMATICS/18.12.1696
B. J. Haas, A. L. Delcher, J. R. Wortman, S. L. Salzberg, DAGchainer: a tool for mining segmental genome duplications and synteny Bioinformatics. ,vol. 20, pp. 3643- 3646 ,(2004) , 10.1093/BIOINFORMATICS/BTH397
Núria Setó-Salvia, Federico Sánchez-Quinto, Eudald Carbonell, Carlos Lorenzo, David Comas, Jordi Clarimón, Using the Neandertal and Denisova Genetic Data to Understand the Common MAPT 17q21 Inversion in Modern Humans Human Biology. ,vol. 84, pp. 633- 640 ,(2012) , 10.3378/027.084.0605
Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfied, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, Sheng Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis, Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biology. ,vol. 3, pp. 1- 22 ,(2002) , 10.1186/GB-2002-3-12-RESEARCH0083
Armando J. Pinho, Diogo Pratas, Paulo J. S. G. Ferreira, Bacteria DNA sequence compression using a mixture of finite-context models ieee signal processing workshop on statistical signal processing. pp. 125- 128 ,(2011) , 10.1109/SSP.2011.5967637