STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
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DOI：
10.1186/1471-2105-10-41
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发表时间：
2009-01-30
影响因子：
3
通讯作者：
Frickenhaus, Stephan
中科院分区：
文献类型：
--
作者：
Kraemer, Lars;Beszteri, Bank;Gaebler-Schwarz, Steffi;Held, Christoph;Leese, Florian;Mayer, Christoph;Poehlmann, Kevin;Frickenhaus, Stephan
微卫星是一种分析能力很强的DNA标记，广泛应用于群体遗传学、遗传作图和法医学研究。目前可用的用于高通量MS设计的软件解决方案（i）在检测和区分不完美和完美MS方面具有缺点，（ii）缺乏通常必要的交互式设计步骤，以及（iii）不允许开发用于多重扩增的引物。我们提出了一套新的工具，实现扩展的STADEN包，它提供了灵活的序列分析工作流程的骨干功能。将重叠读段组装成独特重叠群的可能性（由STADEN包的基本功能提供）对于避免产生冗余标记是重要的，这是大多数其他类似工具所缺少的特征。我们对STADEN包的扩展提供了以下功能，以促进微卫星（以及小型卫星）标记设计：新模块（i）将最先进的串联重复检测和分析软件PHOBOS集成到工作流程中，（ii）提供两个单独的重复检测步骤-具有不同的搜索标准-一个用于在测序读数的组装期间掩蔽重复区域，另一个用于设计重复，MS候选基因座的侧翼引物，（iii）将广泛使用的引物设计程序PRIMER 3纳入STADEN工作流程，使微卫星侧翼引物的交互式设计和可视化成为可能，以及（iv）提供找到最佳基因座和引物对组合的功能，用于多重引物设计。此外，我们的扩展包括一个用于将分析结果存储在SQLite数据库中的模块，为从STADEN包内部和外部访问数据提供透明的解决方案。STADEN软件包通过我们的模块增强为一个高度灵活，高通量，交互式工具，用于常规和多重微卫星标记设计。它为用户提供了对工作流程的详细控制，使手动和自动分析步骤的灵活组合成为可能。该软件在OpenBSD许可证下可用。我们的自动化标记设计工作流程的高效率已在三个微卫星开发项目中得到证实。
Microsatellites (MSs) are DNA markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant markers, a feature missing from most other similar tools. Our extensions to the STADEN package provide the following functionality to facilitate microsatellite (and also minisatellite) marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps – with different search criteria – one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package. The STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex microsatellite marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License. The high efficiency of our automated marker design workflow has been confirmed in three microsatellite development projects.
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影响因子：
4.9
作者：
Dimsoski, P;Toth, GP;Bagley, MJ
通讯作者：
Bagley, MJ
影响因子：
5.8
作者：
Robinson, AJ;Love, CG;Edwards, D
通讯作者：
Edwards, D
影响因子：
7.7
作者：
Faircloth, Brant C.
通讯作者：
Faircloth, Brant C.
DOI：
10.1111/j.1471-8286.2004.00591.x
发表时间：
2004-03-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
Evans, KM;Hayes, PK
通讯作者：
Hayes, PK
影响因子：
2.7
作者：
Fukuoka, H;Nunome, T;Kojima, A
通讯作者：
Kojima, A