期刊文献+

多序列渐进比对算法及其改进算法的研究与比较 被引量:3

Study and comparison of multiple sequence progressive alignment algorithm and its reformative algorithms
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摘要 多序列比对是一种重要的生物信息学工具,在生物的进化分析以及蛋白质的结构预测方面有着积极的意义.以ClustalW为代表的渐进式多序列比对算法在这个领域取得了很大的成功,成为应用最为广泛的多序列比对程序.但其固有的缺陷阻碍了比对精度的进一步提高,近年来出现了许多渐进式比对算法的改进算法,并取得良好的效果.本文选取了其中比较有代表性的几种算法对其基本比对思想予以描述,并且利用多序列比对程序平台BAliBASE和仿真程序ROSE对它们的精度和速度分别进行了比较和评价. Multiple sequence alignment is one of the essential tools for studying bio-informatics. It plays an active and significant role in the aspect of evolution analysis and protein structure prediction. Multiple sequence progressive alignment algorithm represented by Clustalw had been achieved great success in this research field, and had made it to be used most widely. However, the inherent disadvantages of the program had encumbered the further improvement of alignment efficiency. As a result, many improved progressive methods were developed in recent years, and received good results. In this paper, some of the representative methods were selected, and basic ideas of them were sketched and discussed. The efficiency and speed of these methods were compared and evaluated through the use of BALiBASE and the simulation program ROSE.
出处 《大连大学学报》 2005年第2期48-53,共6页 Journal of Dalian University
基金 国家自然科学基金重大计划资助项目(90410012) 国家973计划资助项目(19990328) 大连市科技基金资助项目(200206) 大连理工大学研究生院博士生联合培养计划项目(0221) 大连大学博士生联合培养资助项目(0303023)
关键词 生物信息学 多序列比对 渐进式比对 生物进化 结构预测 蛋白质 bio-informatics multiple sequence alignment progressive alignment BAliBASE
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参考文献9

  • 1[1]OSAMU GOYOH.Multiple sequence alignment: algorithms and applications[J]. Adv. Biophys,1999,36:159-206.
  • 2郭卫斌,施保昌,王能超.多重生物序列对准及其算法综述[J].高技术通讯,2001,11(6):96-102. 被引量:8
  • 3[3]JULIE D.THOMPOSN, et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting ,positon-specific gap penalties and weight matrix choice[J]. Nucleic. Acids. Research, 1994,22: 4673-4680.
  • 4[4]OSAMU GPTOH. Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments[J]. J. Mol. Biol, 1996 ,264: 823-838.
  • 5[5]KAZUTAKA KATOH,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform [J]. Nucleic.Acids.Research,2002,30: 3059-3066.
  • 6[6]ROBERT C.EDGAR. MUSCLE: multiple sequence alignment with high accuracy and high throughput[J]. Nucleic. Acids. Research, 2004,32: 1792-1797.
  • 7[7]CEDRIC NOTREDAME. T-COFFEE: A Novel Method for Fast and Accurate Multiple Sequence Alignment[J]. J. Mol. Biol, 2000,302: 205-217.
  • 8[8]ANNE BAHR, JULIE D.THOMPSON,et al. BAliBASE(Benchmark Alignment database): enhancements for repeats ,transmembrance sequence and circular permutations[J]. Nucleic.Acids.Research,2001,29: 323-326.
  • 9[9]JENE STOYE,et al. Rose: generating sequence families[J]. Bioinformatics, 1998,14: 157-163.

二级参考文献4

共引文献7

同被引文献31

  • 1殷志祥,张家秀.神经网络在蛋白质结构预测中的应用[J].中国科技信息,2005(11):28-29. 被引量:3
  • 2方慧生,相秉仁,安登魁.改进Madaline学习算法预测蛋白质二级结构[J].中国药科大学学报,1996,27(6):366-369. 被引量:17
  • 3司徒浩臻,赵聚雪,许龙飞.基于遗传算法的多序列比对算法研究[J].微计算机信息,2006(06Z):284-286. 被引量:7
  • 4T K Attwood,D J Parry-Smith,罗静初.生物信息学概论.北京大学出版社.2002.
  • 5Jens Stoye ,Multiple sequence alignment with the divide-and- conquer method Gene 211,1998:45 - 56.
  • 6M Wallace, Gordon Blackshields,Desmond G Higgins, Multiple sequence alignments,Current Opinion in Structural Biology,2005, 15:261 - 266.
  • 7Camproux AC,Tuffery P,Chevrolat JP,et al.Hidden Markov model approach for identifying the modular framework of the protein backbone.Protein Eng JT-Protein engineering,1999,12:1063-73.
  • 8Alexandrov V,Gerstein M.Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.BMC Bioinformatics JT-BMC bioinformatics[ electronic resource],2004,5:2.
  • 9Williams A,Gilbert DR,Westhead DR.Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing.Protein Eng JT-Protein engineering,2003,16:913-23.
  • 10Poon TC,Hui AY,Chan HL,et al.Prediction of liver fibrosis and cirrhosis in chronic hepatitis B infection by serum proteomic fingerprinting:a pilot study.Clin Chem JT-Clinical chemistry,2005,51:328 -35.

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