Arner Erik, Tammi Martti T, Tran Anh-Nhi, Kindlund Ellen, Andersson Bjorn
Karolinska Institute, Center for Genomics and Bioinformatics, Stockholm, Sweden.
BMC Bioinformatics. 2006 Mar 20;7:155. doi: 10.1186/1471-2105-7-155.
Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem.
We have developed DNPTrapper, a shotgun sequence finishing tool, specifically designed to address the problems posed by the presence of repeated regions in the target sequence. The program detects and visualizes single base differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. The program is available under an Open Source license.
With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.
由于存在复杂的重复区域，许多基因组计划未能完成。完成测序是最耗时的步骤，而目前的完成工具在设计时并未特别关注重复问题。
我们开发了DNPTrapper，一种鸟枪法序列完成工具，专门设计用于解决目标序列中存在重复区域所带来的问题。该程序可检测并可视化几乎相同的重复拷贝之间的单碱基差异，并提供在一个工作会话中快速解析复杂区域所需的概览和灵活性。使用数据库可存储和处理大量数据，并允许查看哺乳动物大小的基因组。该程序根据开源许可提供。
使用DNPTrapper，可以分离以前认为无法解析的重复区域，并且以前需要数天或数周才能完成的任务现在可以在数小时甚至数分钟内解决。
