MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers
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DOI：
10.1186/1471-2105-7-227
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发表时间：
2006-04-27
影响因子：
3
通讯作者：
Day, Ian N. M.
中科院分区：
文献类型：
--
作者：
Gaunt, Tom R.;Rodriguez, Santiago;Day, Ian N. M.
背景：各种软件工具可用于显示多个单核苷酸多态性之间的成对连锁不平衡。HapMap项目也在他们的网站上展示了这些图形。然而，这些方法是有限的，在他们使用的数据从multiallelic标记，并提供有限的信息在图形form.Results：我们已经开发了一个软件包（MIDAS - Multiallelic Interallelic不平衡分析软件）的估计和图形显示的等位基因间连锁不平衡。在许多基因座（包括单核苷酸多态性、微卫星、小卫星和单倍型）的重叠群（或任何组）中的任何类型的多等位基因基因座的所有成对组合之间，分析每个等位基因组合（来自两个基因座中的每一个的一个等位基因）的连锁不平衡。数据以新颖和信息丰富的方式以图形方式呈现，也可以以表格形式导出用于其他分析。这种方法有利于可视化模式的连锁不平衡的基因组区域，分析不同的等位基因之间的关系multiallelic标记和推断模式的进化和selection.Conclusion：MIDAS是一个连锁不平衡分析程序，具有全面的图形用户界面提供新颖的观点之间的连锁不平衡模式的所有类型的multiallelic和biallelic标记。
Background: Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form.Results: We have developed a software package (MIDAS - Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection.Conclusion: MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.