Software for automated analysis of DNA fingerprinting gels
Software for automated analysis of DNA fingerprinting gels
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DOI：
10.1101/gr.904303
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发表时间：
2003-05-01
期刊：
影响因子：
7
通讯作者：
Marra, MA
中科院分区：
文献类型：
--
作者：
Fuhrmann, DR;Krzywinski, MI;Marra, MA
在这里，我们描述的软件工具，用于自动检测的DNA限制性片段上解决琼脂糖指纹凝胶。我们提出了一个数学模型的限制性片段的位置和形状作为片段大小的函数，与模型参数确定经验从“标记”泳道包含分子大小的标准。限制性片段的自动识别涉及几个步骤，包括：图像预处理，以将数据置于与线性模型一致的形式;标记泳道分析，用于确定模型参数;以及数据泳道分析，用于检测限制性片段多重体同时确定幅度曲线的过程，该幅度曲线描述了限制性片段幅度作为迁移率的函数。在对细菌人工染色体（BAC）克隆进行指纹和测序的验证实验中，限制性片段鉴定的灵敏度和特异性超过96%，限制性片段大小从600个碱基对（bp）到30，000 bp不等。这套软件工具集成套件用MATLAB编写，统称为BandLeader，在BC癌症机构基因组科学中心（GSC）和华盛顿大学基因组测序中心使用，并已提供给Wellcome Trust桑格研究所和Whitehead研究所。在GSC的生产模式中使用，BandLeader已被用于对小鼠，大鼠，牛和白杨指纹图谱项目的850，000多个BAC克隆进行自动限制性片段鉴定。
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.