Computer Science ›› 2019, Vol. 46 ›› Issue (2): 301-305.doi: 10.11896/j.issn.1002-137X.2019.02.046

• Interdiscipline & Frontier • Previous Articles     Next Articles

Quasispecies Reconstruction Algorithm Based on Color Coding Technology

HUANG Dan1, WU Jing-li1,2,3   

  1. College of Computer Science and Information Technology,Guangxi Normal University,Guilin,Guangxi 541004,China1
    Guangxi Key Laboratory of Multi-source Information Mining & Security,Guangxi Normal University,Guilin,Guangxi 541004,China2
    Guangxi Collaborative Innovation Center of Multi-source Information Integration and Intelligent Processing,Guilin,Guangxi 541004,China3
  • Received:2017-11-23 Online:2019-02-25 Published:2019-02-25

Abstract: The reconstruction of viral quasispecies haplotypes contributes to know about the structure of viral gene-tic,and is of great significance for vaccine preparation and antiviral therapy.In this paper,a weighted fragment conflict graph was constructed by introducing fuzzy distance,and a viral quasispecies haplotypes reconstruction algorithm CWSS was proposed based on color coding technology.Firstly,the CWSS algorithm preprocesses thefragment conflict graph in accordance with a given threshold.Secondly,under the condition that adjacent vertices must have different colors,all vertices of the graph are colored according to their sum of edge weigh and saturation value.Finally,quasispecies haplotypes are obtained by assembling the fragment with the same color.The time complexity of the CWSS algorithm is O(m2n+mn).Simulated sequencing fragment were adopted to compare the reconstruction performance and quality of the CWSS algorithm and the Dsatur one.The experimental results show that CWSS algorithm can obtain more accurate quasispecies and higher reconstruction performance than Dsatur algorithm.

Key words: Color coding, Fuzzy distance, Haplotype, Quasispecies, Weighted graph

CLC Number: 

  • TP301
[1]EIGEN M,SCHUSTER P.Hypercycle-principle of natural self-organization.a.emergence of hypercycle[J].Naturwissenschaften,1977,64(11):541-565.
[2]ANDINO R,DOMINGO E.Viral quasispecies[J].Virology, 2015,479-480(1):46-51.
[3]DOMINGO E,SHELDON J,PERALES C.Viral quasispecies evolution[J].Microbiology & Molecular Biology Reviews Mmbr,2012,76(2):159-216.
[4]COX R J,BROKSTAD K A,OGRA P.Influ-enza virus:immunity and vaccination strategies.Comparison of the immune response to inactivated and live,attenuated influenza vaccines[J].Scandinavian Journal of Immunology,2004,59(1):1-15.
[5]LAURING A S,ANDINO R.Quasispecies theory and the behavior of RNA viruses[J].Plos Pathogens,2010,6(7):e1001005.
[6]BU D,TANG H.Quasispecies reconstruction based on vertex coloring algorithms[C]∥IEEE International Conference on Bioinformatics and Biomedicine.Washington D.C:IEEE Co-mputer Society,2014:63-66.
[7]ERIKSSON N,PACHTER L,MITSUYA Y,et al.Viral popula- tion estimation using pyrosequencing[J].Plos Computational Bio-logy,2008,4(5):e1000074.
[8]MANCUSO N,TORK B,SKUMS P,et al.Viral Quasispecies Reconstruction from Amplicon 454 Pyrosequencing Reads[C]∥IEEE International Conference on Bioinformatics and Biomedicine Workshops.Washington D.C:IEEE Computer Society,2011:94-101.
[9]ZAGORDI O,BHATTACHARYA A,ERIKSSON N,et al. ShoRAH:estimating the genetic diversity of a mixed sample from next-generation sequencing data[J].Bmc Bioinformatics,2011,12(1):1-5.
[10]HUANG A,KANTOR R,DELONG A,et al.QColors:An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads[J].Silico Biology,2011,11(5-6):193-201.
[11]BRON C,KERBOSCH J.Algorithm 457:finding all cliques of an undirected graph[J].Communications of the Acm,1973,16(9):575-576.
[12]METZKER M L.Sequencing technologies-the next generation[J].Nature Review Genetic,2010,11(1):31-46.
[13]POH W T,XIA E,CHININMANU K,et al.Viral quasispecies inference from 454 pyrose-quencing[J].BMC Bioinformatics,2013,14(1):355.
[14]ALTSCHUL S F,GISH W,MILLER W,et al.Basic local alignment search tool[J].Journal of Molecular Biology,1990,215(3):403-410.
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