BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as “query” or “target” in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program.

  Over the years, modern sequencing platforms have been generating genome information exponentially, and the number of genes with annotated function is increasing very rapidly as the bioinformatics field advances. Next-generation sequencing technologies have allowed researchers to obtain sequences from whole genome or transcriptome easily in less time and in a cost-effective manner. Thus, effective bioinformatics tools are required to curate the obtained sequence data to match the annotated gene information in the public database. Since the introduction of the Basic Local Alignment Search Tool (BLAST) program in 1990 (Altschul et al., 1990), this has been one of the most widely used bioinformatics programs. The algorithm of BLAST program approximates sequence alignment by optimizing the local similarities between sequences by heuristic method. The BLAST algorithm had been further implemented into more advanced programs, such as WU-BLAST (Chao et al., 1992) and ScalaBLAST (Oehmen et al., 2013), but the most fundamental and earliest implementation of BLAST is by NCBI as a free web-based service, which is used by researchers worldwide. However, researchers cannot use their own sequence data with the web-based NCBI-BLAST program if the data exceed a size limit during the query sequence upload process, effectively precluding the analysis of large sequence data, such as whole transcriptome data sets. If researchers want to run BLAST on their own sequences, they will have to create a BLAST database in advance. However, NCBI-BLAST does not support custom database creation; hence, researchers must download the NCBI-BLAST program to analyze their own sequences. This introduces another barrier to accessibility, as executing the downloaded program requires a fairly advanced computational skill entailing the use of the command line interface (CLI).

  The output of the BLAST program can be visualized using dot plots. A dot plot is a graphical representation of sequence similarities between two biological samples of proteins or nucleotides (Gibbs and McIntyre, 1970). Dot plot is very efficient for the analysis of structural variations, such as duplication, inversion, and deletion between two sequences, as the results are displayed in a dot plot matrix. Dozens of dot plot programs are available online.

  NBLAST program is a graphical user interface (GUI)-based BLAST program and dot plot viewer for similarity analysis between two sequences. Researchers can create their own database for a BLAST analysis and dot plot visualization. Because databases can hold a massive amount of data, researchers can analyze their own whole genome or transcriptome sequences using the NBLAST program with ease. Moreover, this program employs a two-way system that allows the created database to be used as either the ‘query’ or the ‘target’ sequence for BLAST analysis, which is not possible on the web-based NCBI-BLAST program. Prior to the current NBLAST program, Du et al. (2019) reported a similar program, BlastGUI, that runs BLAST analysis using the two-way method. We improved the two-way BLAST analysis system by adding a dot plot viewing function in NBLAST, to enable researchers to carry out BLAST analysis on multiple sequences and generate a dot plot between two sequences in a single program.