Dotplotic: a lightweight visualization tool for BLAST + alignments and genomic annotations

• Published in: BMC bioinformatics Vol. 26; no. 1; pp. 222 - 12
• Main Authors: Miyazawa, Hideyuki, Oda, Toshiyuki
• Format: Journal Article
• Language: English
• Published: London BioMed Central 27.08.2025; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Alignment; Animal behavior; Annotations; Bioinformatics; Biological research; Biology, Experimental; Biomedical and Life Sciences; BLAST; Comparative analysis; Computational Biology - methods; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Dot plot; Explosions; Gene sequencing; Genes; Genome comparison; Genomes; Genomics; Genomics - methods; Life Sciences; Methods; Microarrays; Molecular Sequence Annotation - methods; Perl; Programming languages; Python; Sequence Alignment - methods; Software; User interface; Visualization; Visualization (Computers); Japan; Perl; Dot plot; BLAST; Genome comparison
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-025-06255-5

With the development of sequencing technologies, chromosome-level genome assemblies have become increasingly common across various organisms, including non-model species. BLAST + is one of the most widely used bioinformatics tools for computing sequence alignments, offering numerous optimizations for speed and scalability. Dot plots, which visualize the similarity between two sequences, are widely used in biological research. However, while many dot plot-generating programs exist, most rely on their own alignment algorithms, and it is uncommon to visualize external BLAST results directly. Here, we present Dotplotic, a lightweight Perl program that generates dot plot-like visualizations based on BLAST output in tabular format. Dotplotic visualizes each alignment as a line connecting the start and end points of the query and subject sequences, with a gradient color indicating sequence identity. It allows users to overlay annotation data from external files onto the plot. Although command-line-based, Dotplotic is implemented as a single script using only core Perl modules, making it easy to install and run across platforms. The program supports standard input for both BLAST results and annotation files, enabling flexible visualization under various conditions, such as filtering specific alignments or displaying selected genomic features like genes or repeats. Dotplotic is an efficient, portable, and easy-to-use visualization tool that enhances the exploration of sequence alignments and serves as a valuable resource for both bioinformatics and broader biological research.