期刊文献+
任意字段
题名或关键词
题名
关键词
文摘
作者
第一作者
机构
刊名
分类号
参考文献
作者简介
基金资助
栏目信息

分子遗传学数据分析和处理平台的设计与实现

The Design of Data Analysis and Processing Platform for Molecular Genetics
下载PDF
导出
摘要 目的开发一个在高性能计算机的Linux环境下运行,基于B/S模式的分子遗传学数据分析与处理平台。方法以Apache HTTP服务器为平台的WEB服务器,采用Perl语言整合许多遗传学数据分析软件和工具包,针对不同的SNPs变异数据,以提示方式简化数据输入格式和参数设置,经平台处理的结果以表格、文本或图像格式输出。结果该平台实现了连锁不平衡的计算和绘制、挑选标签SNP和疾病对照设计或传递不平衡设计的关联分析,以及对一些群体遗传数据的估计等功能,操作简单,数据分析速度快。结论该平台作为一个整合的遗传学研究辅助工具,克服了当前遗传分析软件或工具包在操作使用方面的不足,为遗传学研究者提供方便。目前该平台正处于测试阶级,运行状态良好。 Objective To design the data analysis and processing platform for molecular genetics base on browser/server mode which runs in Linux operating system on the high-powered computer. Methods The server of platform is Apache HTI＇P server. Perl language was used to integrate with some molecular genetics analyzing software and simplify the input format and preset parameter according to different SNPs data. The analyzed result is outputted with the table, text or image formats. Results The platform can be handled easily and quickly when it is used to analyze SNPs data; it can be used to calculate linkage disequilibrium, select tag SNPs, associate with the study with case-control design or transmission disequilibrium test and estimate some population genetics data. Conclusion The platform overcomes the non-friendly property of most of molecular genetics analyzing software. It is considered as a combined platform to provide convenience analyzing tools for many genetics researchers.
作者 闫微 郭云波 王胜军 刘娜 邓亲恺
机构地区 南方医科大学基础医学院生物信息学研究室
出处 《热带医学杂志》 CAS 2008年第3期225-228,共4页 Journal of Tropical Medicine
关键词 SNPS 遗传变异 关联分析 群体遗传 生物信息学 SNPs genetic variation association study population genetics bioinformatics
分类号 Q811.4 [生物学—生物工程]
  • 相关文献

参考文献18

  • 1International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs [J]. Nature,2007, 449 : 851-861.
  • 2Raymond M,Rousset F. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism [J]. Heredity, 1995,86 : 248-249.
  • 3Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): An integrated software package for population genetics data analysis [J ]. Evolutionary Bioinformatics Online, 2005, 1 : 47 -50.
  • 4Barrett JC, Fry B, Mailer J, et al. Haploview : analysis and visualization of LD and haplotype maps [J]. Bioinformatics, 2005,21 (2) : 263-265.
  • 5Purcell S, Neale B, Todd-Brown K,et al. PUNK: a tool set for whole-genome association and population-based linkage analyses [J ]. Am J Hum Genet, 2007,81 (3) : 559-575.
  • 6Slatkin M, Rannala B. Estimating the age of alleles by use of intraallelic variability [J]. Am J Hum Genet, 1997,60:447- 458.
  • 7Stajich JE, Block D, Boulez K, et al. The bioperl toolkit : Perl modules for the life sciences [J ]. Genome Research, 2002,12 (10) : 1611-1618.
  • 8Stajich JE, Hahn MW. Disentangling the effects of demography and selection in human history [J]. Mol Biol Evol,2005,22 ( 1 ) : 63-73.
  • 9Stephens M, Scheet P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation [ J ]. Am J Hum Genet, 2005,76 ( 3 ) : 449- 462.
  • 10Clark AG. Inference of haplotypes from PCR-amplified samples of diploid populations [ J ], Mol Biol Evol, 1990,7 : 111-122.

二级参考文献22

  • 1The International HapMap Consortium. The international HapMap project[J]. Nature,2003, 426:789-796.
  • 2Shastry BS. SNP alleles in human disease and evolution[J]. J Hum Genet,2002, 47:561-566.
  • 3Marth G, Yeh R, Minton M, et al. Single-nucleotide polymorphisms in the public domain: how useful are they?[J]. Nat Genet,2001, 27:371-372.
  • 4Sachidanandam R, Weissman D, Schmidt SC, et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms[J]. Nature,2001 409:928-933.
  • 5Environmental Genome Project. http://www.niehs.nih.gov/envgenom/snpsdb.htm, 2004-09-09.
  • 6About the Program in Genomic Applications(PGA). http://pga.gs.washington.edu/info.html, 2004-01-12.
  • 7Shi J, Xi H, Wang Y, et al. Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units[J]. Proc Natl Acad Sci USA,2003,100:8331-8336.
  • 8Flavell AJ, Bolshakov VN, Booth A, et al. A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach[J]. Nucleic Acids Res,2003, 31:19.
  • 9Carlson CS, Eberle MA, Kruglyak L, et al. Mapping complex disease loci in whole-genome association studies[J]. Nature,2004,429:446-452.
  • 10Zhang W, Collins A, Maniatis N, et al. Properties of linkage disequilibrium (LD) maps[J]. Proc Natl Acad Sci USA,2002,99:17004-17007.

共引文献15

热带医学杂志
2008年 第3期

相关作者

内容加载中请稍等...

相关机构

内容加载中请稍等...

相关主题

内容加载中请稍等...

浏览历史

内容加载中请稍等...
;
使用帮助 返回顶部