Dowd Scot E, Zaragoza Joaquin, Rodriguez Javier R, Oliver Melvin J, Payton Paxton R
Livestock Issues Research Unit, Agriculture Research Service, USDA, Lubbock, TX, USA.
BMC Bioinformatics. 2005 Apr 8;6:93. doi: 10.1186/1471-2105-6-93.
BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality.
W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files.
W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from http://liru.ars.usda.gov/mainbioinformatics.html. With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum.
BLAST是基因研究中最常用且实用的工具之一。本文介绍了一款我们称为Windows.NET分布式基本局部比对搜索工具包（W.ND - BLAST）的软件应用程序，它通过在Windows桌面环境中提高可用性、故障恢复能力和可扩展性来增强BLAST的实用功能。我们的目标是开发一个易于使用、容错且高通量的BLAST解决方案，该方案集成了一个具有管理和注释功能的全面的BLAST结果查看器。
W.ND - BLAST是一个基于Windows的综合性软件工具包，面向研究人员，包括那些计算机技能有限的人员，并通过将BLAST查询分布到局域网（LAN）中的任意数量的基于Windows的机器上，提高BLAST的性能。W.ND - BLAST为BLAST数据库创建、BLAST执行、BLAST输出评估和BLAST结果导出提供直观的图形用户界面（GUI）。该软件还提供了多层容错和故障恢复功能，以防止节点或主机器出现故障时数据丢失。本文阐述了W.ND - BLAST的功能。当将任务分发给12台性能相同的远程计算机时，W.ND - BLAST显示出接近100%的性能效率。一个在一台普通机器上需要662.68分钟（11小时）的高通量BLAST作业，在分发给17个节点（包括性能较低的机器）时，44.97分钟就完成了。最后，有一个全面的高通量BLAST输出查看器（BOV）和注释引擎组件，它提供将BLAST命中结果全面导出到文本文件、带注释的fasta文件、表格或关联文件的功能。
W.ND - BLAST提供了一个交互式工具，使科学家能够轻松利用其可用的计算资源进行高通量和全面的序列分析。W.ND - BLAST的安装包可从http://liru.ars.usda.gov/mainbioinformatics.html免费下载。注册后软件免费，并提供安装、联网和使用说明以及一个支持论坛。
