He Ji, Dai Xinbin, Zhao Xuechun
Bioinformatics Lab, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
BMC Bioinformatics. 2007 Feb 9;8:53. doi: 10.1186/1471-2105-8-53.
BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming.
Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration.
PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at http://bioinfo.noble.org/plan/. The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users.
BLAST搜索广泛用于序列比对。搜索结果通常用于各种功能和比较基因组学任务，如注释未知序列、研究基因模型以及比较两个序列集。测序技术的进步给大规模序列数据的高通量分析带来了挑战。存在许多用于高效BLAST搜索的程序和硬件解决方案，但缺乏用于挖掘和个性化管理结果的通用软件解决方案。系统地审查结果并识别感兴趣的信息仍然繁琐且耗时。
个人BLAST导航器（PLAN）是一个多功能的网络平台，可帮助用户执行各种个性化的BLAST前后任务，包括：（1）查询和目标序列数据库管理；（2）自动化高通量BLAST搜索；（3）结果的索引和搜索；（4）在线过滤结果；（5）在收藏类别中管理个人感兴趣的结果；（6）自动化序列注释（如NCBI NR和基于本体的注释）。PLAN默认集成了Active Motif Inc.提供的基于硬件的Decypher BLAST解决方案，与传统BLAST软件相比，效率大大提高。BLAST结果通过电子表格和图表可视化，并且支持全文搜索。BLAST结果和序列注释可以部分或全部以各种格式导出，包括Microsoft Excel和FASTA。序列和BLAST结果按项目组织，其数据发布级别由注册的项目所有者控制。此外，所有分析功能都提供给未注册的公共用户。
PLAN已被证明是该社区在自动化高通量BLAST搜索方面的宝贵补充，更重要的是，在基于序列比对结果的知识发现、管理和共享方面。PLAN网络界面独立于平台，易于配置且能够全面扩展，并且用户直观。学术用户可在http://bioinfo.noble.org/plan/免费使用PLAN。本地部署的源代码根据免费许可提供。为学术用户提供有关系统使用、安装、配置和定制的全面支持。
