CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes.
CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes.
复制标题
DOI：
10.1186/1471-2105-12-27
复制
发表时间：
2011-01-20
影响因子：
3
通讯作者：
Falque M
中科院分区：
文献类型：
--
作者：
Gauthier F;Martin OC;Falque M
在减数分裂过程中，同源染色体通过交换形成片段。这一现象受到高度管制;特别是，交叉点沿着物理地图不均匀地分布，很少出现在非常接近的地方，这一特性被称为"干扰"。交叉位置形成的模式提供了关于交叉是如何形成的线索。在包括酵母、番茄、拟南芥和小鼠在内的几种生物中，据信交叉通过至少两种途径形成，一种干扰，另一种不干扰。我们已经开发了一个软件包-"CODA"，交叉分布分析仪-它允许一个定量表征交叉模式拟合干扰模型的实验数据。提供了两个系列的干扰模型：“伽马”模型和“梁膜”模型。用户可以指定单通道或双通道建模，软件包推断模型的参数及其置信区间。CODA可以以连续交叉位置或标记基因分型的形式处理由二价体或配子测量产生的数据。我们用小麦、玉米和小鼠的数据说明了这种可能性。CODA扩展了迄今为止可以分析的交叉数据类型，以包括配子数据（而不仅仅是二价体/四分体）。它还将使用户能够根据光束-胶片模型进行分析。CODA实现了该模型的复杂物理和数学，并使用汇总统计来克服迄今为止阻碍其使用的可计算可能性的缺乏。
During meiosis, homologous chromosomes exchange segments via the formation of crossovers. This phenomenon is highly regulated; in particular, crossovers are distributed heterogeneously along the physical map and rarely arise in close proximity, a property referred to as "interference". Crossover positions form patterns that give clues about how crossovers are formed. In several organisms including yeast, tomato, Arabidopsis, and mouse, it is believed that crossovers form via at least two pathways, one interfering, the other not. We have developed a software package - "CODA", for CrossOver Distribution Analyzer - which allows one to quantitatively characterize crossover patterns by fitting interference models to experimental data. Two families of interfering models are provided: the "gamma" model and the "beam-film" model. The user can specify single or two-pathways modeling, and the software package infers the model's parameters and their confidence intervals. CODA can handle data produced from measurements on bivalents or gametes, in the form of continuous crossover positions or marker genotyping. We illustrate the possibilities on data from Wheat, corn and mouse. CODA extends the kind of crossover data that could be analyzed so far to include gametic data (rather than only bivalents/tetrads) when using two-pathways modeling. It will also enable users to perform analyses based on the beam-film model. CODA implements that model's complex physics and mathematics, and uses a summary statistic to overcomes the lack of a computable likelihood which has hampered its use till now.
登录
查看更多内容
ATMUS81在A. thaliana中对干扰不敏感的交叉中的作用。
影响因子：
4.5
作者：
Berchowitz, Luke E.;Francis, Kirk E.;Bey, Alexandra L.;Copenhaver, Gregory P.
通讯作者：
Copenhaver, Gregory P.
影响因子：
2.6
作者：
Anderson, L. K.;Stack, S. M.
通讯作者：
Stack, S. M.
影响因子：
3.3
作者：
Saintenac, Cyrille;Falque, Matthieu;Sourdille, Pierre
通讯作者：
Sourdille, Pierre
影响因子：
11.6
作者：
Falque, Matthieu;Anderson, Lorinda K.;Martin, Olivier C.
通讯作者：
Martin, Olivier C.
影响因子：
9.8
作者：
Housworth, EA;Stahl, FW
通讯作者：
Stahl, FW