PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories
PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories
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DOI：
10.1186/1471-2199-8-77
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发表时间：
2007-09-17
影响因子：
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通讯作者：
Wartiovaara, Kirmo
中科院分区：
文献类型：
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作者：
Angers-Loustau, Alexandre;Rainy, Jeffrey;Wartiovaara, Kirmo
背景资料：大多数分子生物学实验，以及与这一研究领域相关的技术，都涉及大量的分子克隆形式的工程。像所有形式的工程，关于起始材料的完美信息是成功完成设计和strategies.Results的关键：我们已经生成了一个程序，允许完整的模拟克隆实验。从一级DNA序列开始，PlasmaDNA寻找限制性位点、开放阅读框、引物退火序列和各种共同结构域。用户可以轻松扩展数据库，以满足其最常见的克隆需求。PlasmaDNA可以同时管理和图形化地表示多个序列，并将序列末端的突出端（如果有的话）保存在内存中。这意味着可以虚拟消化片段，将消化产物添加到项目中，并将具有相容末端的片段连接在一起以产生新序列。聚合酶链反应（PCR）片段也可以使用引物数据库虚拟生成，自动添加到片段中存在于primers.Conclusion中的任何5'额外序列：PlasmaDNA是一个可在Windows和Apple操作系统上使用的程序，旨在通过构建DNA的可视化图谱来促进分子克隆实验。然后，它允许克隆实验的完整规划和模拟。它还自动更新过程中生成的新序列，这在实践中是一个重要的帮助。在同一文件中保存多个序列的能力也可用于存档每个构建体克隆中涉及的各种步骤和策略。该程序可免费下载，不收费或限制。
Background: Most molecular biology experiments, and the techniques associated with this field of study, involve a great deal of engineering in the form of molecular cloning. Like all forms of engineering, perfect information about the starting material is crucial for successful completion of design and strategies.Results: We have generated a program that allows complete in silico simulation of the cloning experiment. Starting with a primary DNA sequence, PlasmaDNA looks for restriction sites, open reading frames, primer annealing sequences, and various common domains. The databases are easily expandable by the user to fit his most common cloning needs. PlasmaDNA can manage and graphically represent multiple sequences at the same time, and keeps in memory the overhangs at the end of the sequences if any. This means that it is possible to virtually digest fragments, to add the digestion products to the project, and to ligate together fragments with compatible ends to generate the new sequences. Polymerase Chain Reaction (PCR) fragments can also be virtually generated using the primer database, automatically adding to the fragments any 5' extra sequences present in the primers.Conclusion: PlasmaDNA is a program available both on Windows and Apple operating systems, designed to facilitate molecular cloning experiments by building a visual map of the DNA. It then allows the complete planning and simulation of the cloning experiment. It also automatically updates the new sequences generated in the process, which is an important help in practice. The capacity to maintain multiple sequences in the same file can also be used to archive the various steps and strategies involved in the cloning of each construct. The program is freely available for download without charge or restriction.