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NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer.

Jatindra Nath Mohanty1, Swayamprabha Sahoo2, Puspanjali Mishra3

  • 1Department of Botany, School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar 752050, India.

Genomics & Informatics
|October 14, 2022
PubMed
Summary

Scientists can now perform large-scale sequence similarity searches with NBLAST, a new graphical tool that overcomes the upload limitations of web-based Basic Local Alignment Search Tool (BLAST) analysis. NBLAST also offers a dot plot viewer for custom database creation and analysis.

Keywords:
BLASTdatabasedot plotsequence alignmenttwo-way BLAST system

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Basic Local Alignment Search Tool (BLAST) is a fundamental bioinformatics program for sequence similarity searches.
  • Web-based NCBI-BLAST is commonly used, but faces limitations with large datasets like whole genomes or transcriptomes.
  • These limitations hinder scientists needing to analyze extensive biological sequence data locally.

Purpose of the Study:

  • To develop a user-friendly graphical interface for BLAST analysis that overcomes upload size restrictions.
  • To provide researchers with a tool capable of handling large sequence datasets efficiently.
  • To integrate additional functionalities for enhanced sequence analysis.

Main Methods:

  • Development of NBLAST, a graphical user interface (GUI)-based BLAST program.
  • Implementation of a two-way system allowing sequences to be used as either 'query' or 'target'.
  • Integration of a dot plot viewer for similarity analysis and custom database creation.

Main Results:

  • NBLAST successfully overcomes the upload size limitations of web-based BLAST.
  • The program allows users to perform BLAST analysis on large sequence data, including transcriptomes and whole genomes.
  • NBLAST integrates a dot plot viewer, enabling custom database creation and similarity analysis within a single application.

Conclusions:

  • NBLAST provides a convenient and powerful solution for researchers dealing with large-scale sequence data analysis.
  • The tool enhances the capabilities of traditional BLAST analysis by removing size constraints and adding integrated features.
  • NBLAST is accessible online, facilitating broader adoption in the scientific community.