SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence.
SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence.
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DOI：
10.1186/1756-0500-2-148
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发表时间：
2009-07-23
影响因子：
1.8
通讯作者：
Larkin, Denis M
中科院分区：
文献类型：
--
作者：
Donthu, Ravikiran;Lewin, Harris A;Larkin, Denis M
背景技术背景：最近大量哺乳动物的基因组序列和BAC文库的可用性为鉴定可用于创建高分辨率辐射杂交（RH）和基于BAC的比较图谱的比较锚定标记提供了极好的机会。要使用这些地图多物种基因组比较和进化推理，强大的生物信息学工具，需要识别基因组之间共享的染色体区域，并定位进化断点的位置，这是染色体重排的签名。在这里，我们报告了一个自动化的工具，用于识别基因组之间的同源同线性块（HSBs），容忍RH比较地图中常见的错误，并可用于自动化全基因组分析的染色体重排，发生在evolution.FINDINGS：我们开发了一种算法和软件工具（SyntenyTracker），可用于自动定义的HSBs使用成对RH或基于基因的比较地图作为输入。为了验证基本算法的正确实施，SyntenyTracker用于识别牛和人类基因组中的HSB。结果表明，与使用相同规则集手动定义的HSB的一致率为96%。SyntenyTracker与AutoGRAPH synteny工具的比较是使用包含14，380个基因的相同数据集进行的，这些基因在人类和小鼠中具有1：1的同源性。使用这两种工具的结果和SyntenyTracker的优势之间的discredibility reported.CONCLUSION：SyntenyTracker被证明是一个有效的和准确的自动化工具，用于定义HSBs使用的数据集，可能包含轻微的错误，在地图构建方法的限制。SyntenyTracker的效用将变得更加重要的比较基因组学的映射和测序的基因组数量的增加。
BACKGROUND: The recent availability of genomic sequences and BAC libraries for a large number of mammals provides an excellent opportunity for identifying comparatively-anchored markers that are useful for creating high-resolution radiation-hybrid (RH) and BAC-based comparative maps. To use these maps for multispecies genome comparison and evolutionary inference, robust bioinformatic tools are required for the identification of chromosomal regions shared between genomes and to localize the positions of evolutionary breakpoints that are the signatures of chromosomal rearrangements. Here we report an automated tool for the identification of homologous synteny blocks (HSBs) between genomes that tolerates errors common in RH comparative maps and can be used for automated whole-genome analysis of chromosome rearrangements that occur during evolution.FINDINGS: We developed an algorithm and software tool (SyntenyTracker) that can be used for automated definition of HSBs using pair-wise RH or gene-based comparative maps as input. To verify correct implementation of the underlying algorithm, SyntenyTracker was used to identify HSBs in the cattle and human genomes. Results demonstrated 96% agreement with HSBs defined manually using the same set of rules. A comparison of SyntenyTracker with the AutoGRAPH synteny tool was performed using identical datasets containing 14,380 genes with 1:1 orthology in human and mouse. Discrepancies between the results using the two tools and advantages of SyntenyTracker are reported.CONCLUSION: SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies. The utility of SyntenyTracker will become more important for comparative genomics as the number of mapped and sequenced genomes increases.