Submitted to: BMC Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 8, 2005
Publication Date: April 8, 2005
Citation: Dowd, S.E., Zaragoza, J, Rodriguez, J.R., Oliver, M.J., Payton, P.R. 2005. Windows.NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinformatics. 6:93. Available: http://www.biomedcentral.com/1471-2105/6/93. Interpretive Summary: Bioinformatics is an important field of research. Because of the incredible amount of genetic sequence data derived using current methodologies, existing bioinformatics tools are a considerable bottleneck for researchers. The USDA-ARS Livestock Issues Research Unit performs roughly 20,000 nucleotide database searches weekly and there is a considerable need to reduce the productivity bottleneck. In addition, many of our collaborators are not extremely computer literate. These two issues provided the need for the development of a very user friendly genetic database creation, database search engine, high throughput database search result viewer and curation tool, as well as a genetic sequence annotation toolkit. We developed a Windows network distributed BLAST engine that allows an efficient increase in productivity based upon the number of available workstations in a local network. A comprehensive graphical user interface system allows even the most computer naïve geneticist or molecular biologist to make use of this toolkit for processing genetic sequence data in a logical manner against custom databases or standard databases obtained from various public sources. W.ND-BLAST provides an interactive tool to scientists for easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install script for W.ND BLAST is freely downloadable from http://liru.ars.usda.gov/mainbioinformatics.html. Registration of the software is free and installation, networking, and usage instructions are provided. Contact: firstname.lastname@example.org.
Technical Abstract: This paper describes a software package, W.ND-BLAST, which improves utility and usability and allows for scalability of Basic Local Alignment Search Tool (BLAST). BLAST is one of the most common and useful tools for livestock or any other type of genetic research. Our goal was to develop an easy to use, high-throughput network distributed BLAST solution that incorporates a comprehensive BLAST result viewer, curation tool, and annotation tool. W.ND-BLAST is a Windows based software tool that gives researchers with nominal computer skills the ability to scale their BLAST queries. It also provides intuitive Graphic User Interface (GUI) to analyze and export the resulting output. This paper lays out the functionality W.ND-BLAST provides for distributing BLAST, formatting known databases, and creating text, tabulations, or annotated fasta formatted files from BLAST outputs for further downstream functional analyses. It has a user friendly ability to distribute traditional BLAST queries to available networked Windows based workstations, providing an increase in workstation utilization and a decrease in research time. The included Database Engine (DBE) enables customized creation of databases from any fasta formatted sequence file. Additionally, the BLAST Output Viewer (BOV) and annotation engine components provide exportation of user selected BLAST hits to text files. W.ND-BLAST provides an interactive tool to scientists for easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install script for W.ND BLAST is freely downloadable from http://liru.ars.usda.gov/mainbioinformatics.html. Registration of the software is free and installation, networking, and usage instructions are provided. Contact: email@example.com.