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Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST) - PubMed

  • ️Sat Jan 01 2005

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

Scot E Dowd et al. BMC Bioinformatics. 2005.

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

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Figures

Figure 1
Figure 1

Screenshot: Project Control Panel (PCP). The Project Control Panel (PCP) displays the user's options for W.ND BLAST. This example screenshot shows where the user is able to "Create New Project" by simply entering in a new project name. The "Create New Project" can also be changed to "Load Saved Project" where the user has the option to choose a previous project from the left text box.

Figure 2
Figure 2

Screenshot: Database and BLAST Engine (DBE). This example screenshot displays the Database Engineer, which is used for scanning for child nodes, creating custom databases and distributing existing databases. Within the same interface is the BLAST engine, which is used for executing inputting query sequences, choosing BLAST parameters, and executing BLAST jobs. Also available is the ability to control child nodes during BLAST jobs. Lastly, the user has the option of resuming a failed BLAST.

Figure 3
Figure 3

Screenshot: BLAST Output Viewer (BOV). This example screenshot of the BLAST Output Viewer displays some of the available columns information from an individual BLAST hit. This particular window is displaying the first five hits for a sequence named, "Contig_318." From here the user can move forward or backward through all BLAST output sequences. The user can also click on the "View Alignment" column to bring up the "Sequence Alignment Viewer" window.

Figure 4
Figure 4

Screenshot: Sequence Alignment Viewer. This screenshot of the Sequence Alignment Viewer gives an example the BLAST output for one alignment. The query sequence, midline and hit sequence are displayed in parallel and pair-wise equal can be seen in black

Figure 5
Figure 5

Screenshot: Annotation Engine. The Annotation Engine window shown here gives the user the options to export their data in several different formats. The user can choose from any of the available BLAST output result fields and any available type of output file and associated delimiters.

Figure 6
Figure 6

WND-BLAST Performance. This graph presents the performance of WND-BLAST observed when varying the number of workstations and input sequences. To collect this data, we utilized W.ND-BLAST to perform BLASTx against a 332 MB (formatted size) database with the varying number of input (query) sequences shown.

Figure 7
Figure 7

Workstation Efficiency Percentage with Best Fit trend lines. This graph shows the overall efficiency of performance of the data presented in Figure 1, as the number of machines is increased. Equation 1 from the text is used to generate this data. The linear best fit regressions for the data points are also provided.

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