PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results.
PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results.
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DOI：
10.1186/1471-2105-8-53
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发表时间：
2007-02-09
影响因子：
3
通讯作者：
Zhao X
中科院分区：
文献类型：
--
作者：
He J;Dai X;Zhao X
BLAST搜索被广泛用于序列比对。搜索结果通常用于各种功能基因组学和比较基因组学任务，如注释未知序列，研究基因模型和比较两个序列集。测序技术的进步对大规模序列数据的高通量分析提出了挑战。目前已有许多程序和硬件解决方案用于高效的BLAST搜索，但缺乏用于挖掘和个性化管理结果的通用软件解决方案。系统地审查结果和识别感兴趣的信息仍然是乏味和耗时的。Personal BLAST Navigator （PLAN）是一个多功能的web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)索引和搜索结果，(4)在线过滤结果，(5)管理个人感兴趣的分类结果，(6)自动序列注释（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Decypher硬件的BLAST解决方案，比传统的BLAST软件效率大大提高。BLAST结果通过电子表格和图表可视化，并且可以全文搜索。BLAST结果和序列注释可以部分或全部以各种格式（包括Microsoft Excel和FASTA）导出。序列和BLAST结果在项目中组织，其数据发布级别由注册的项目所有者控制。此外，所有分析功能均提供给公众用户，无需注册。PLAN已经被证明是对自动化高通量BLAST搜索社区的一个有价值的补充，更重要的是，对于基于序列比对结果的知识发现、管理和共享。PLAN web界面是平台独立的，易于配置，能够全面扩展，用户直观。PLAN免费提供给学术用户。本地部署的源代码是在免费许可下提供的。为学术用户提供系统使用、安装、配置和定制的全面支持。
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 . 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.
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影响因子：
5.8
作者：
Grant, JD;Dunbrack, RL;Ochs, MF
通讯作者：
Ochs, MF
影响因子：
5.8
作者：
Mao, CH;Cushman, JC;Weller, JW
通讯作者：
Weller, JW
DOI：
10.1016/s0167-739x(00)00057-1
发表时间：
2001-04-01
期刊：
FUTURE GENERATION COMPUTER SYSTEMS
影响因子：
--
作者：
Braun, RC;Pedretti, KT;Roberts, CA
通讯作者：
Roberts, CA
影响因子：
14.9
作者：
Altschul, SF;Madden, TL;Lipman, DJ
通讯作者：
Lipman, DJ
影响因子：
3
作者：
Dumontier, M;Hogue, CWV
通讯作者：
Hogue, CWV