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基于PC/Linux的核酸序列电子延伸系统的构建及其应用
引用本文:张成岗,孙焕东,欧阳曙光,吴松峰,贺福初.基于PC/Linux的核酸序列电子延伸系统的构建及其应用[J].遗传,2002,24(1):50-54.
作者姓名:张成岗  孙焕东  欧阳曙光  吴松峰  贺福初
作者单位:1.军事医学科学院放射医学研究所; 2.军事医学科学院情报信息研究所,北京100850 1.Beijing Institute of Radiation Medicine; 2.Information Center of Academy of Military Medicine Science,Taiping Road 27,Beijing 100850,P.R.China
基金项目:军事医学科学院科技创新研究启动基金 ( 990 5 10 5 ),国家“86 3”项目 ( 86 3— 10 2— 10— 0 4— 0 4),国家杰出青年科学基金 ( 396 2 0 5 14 ),国家自然科学基金重点项目 ( 39730 310 ,39970 2 47),国家自然科学基金项目 ( 3990 0 0 41、3990 0 0 74)部分资
摘    要:新基因全长cDNA序列的获得常常是分子生物学工作者面临的难题。人类基因组计划及其相关计划的实施导致了大量表达序列标签(EST)的产生。利用一定的生物信息学算法,这些EST序列往往可用来对新基因片段进行延伸。采用Linux操作系统,利用Blast软件和Phrap软件以及EST数据库在微机上构建了EST序列的电子延伸系统,并对来自于人胎肝的11386条EST序列和511条插入片段全长cDNA序列进行了电子延伸,结果显示8373条EST序列和389条插入片段全长cDNA序列得到了程度不等的延伸,部分结果通过RACE实验得到证实。该套系统可高效地、规模化进行EST序列的延伸,可为通过实验获得新基因全长cDNA序列提供重要线索。 Abstract:Normally it is difficult to obtain full-length cDNA sequence of novel genes.More and more expressed sequence tags(ESTs) have been obtained since the start-up of human genome project.Powerful system is badly needed for data mining on these EST sequences.Based on a personal computer coupled with Linux operating system and EST database,the Blast software and Phrap software were used to construct a platform for in silico elongation of ESTs in our lab.The performance was tested using 11386 EST sequences and 511 partial-length cDNA sequences.Results demonstrated that 8373 EST and 389 cDNA sequence were elongated using this system.Thus the platform seems to be a fast way for full-length cDNA sequence cloning of new genes.

关 键 词:表达序列标签  生物信息学  cDNA  微机  电子序列延伸  
文章编号:0253-9772(2002)01-0050-05
修稿时间:2001年2月8日

Construction and Application of an in Silico Elongation System of Nucleic Acid Sequence
ZHANG Cheng-gang ,SUN Huan-dong ,OUYANG Shu-guang ,WU Song-feng ,HE Fu-chu.Construction and Application of an in Silico Elongation System of Nucleic Acid Sequence[J].Hereditas,2002,24(1):50-54.
Authors:ZHANG Cheng-gang  SUN Huan-dong  OUYANG Shu-guang  WU Song-feng  HE Fu-chu
Institution:ZHANG Cheng-gang 1,SUN Huan-dong 2,OUYANG Shu-guang 1,WU Song-feng 1,HE Fu-chu 1
Abstract:Normally it is difficult to obtain full-length cDNA sequence of novel genes.More and more expressed sequence tags(ESTs) have been obtained since the start-up of human genome project.Powerful system is badly needed for data mining on these EST sequences.Based on a personal computer coupled with Linux operating system and EST database,the Blast software and Phrap software were used to construct a platform for in silico elongation of ESTs in our lab.The performance was tested using 11386 EST sequences and 511 partial-length cDNA sequences.Results demonstrated that 8373 EST and 389 cDNA sequence were elongated using this system.Thus the platform seems to be a fast way for full-length cDNA sequence cloning of new genes.
Keywords:bioinformatics  expressed sequence tag  cDNA  in Silico sequence elongation  personal computer  Linux operation system
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