*3.9. Sequence Searches Using Basic Local Alignment Search Tool (BLAST)*

Sequence similarity comparison is a widely used basic bioinformatics tool for the identification of possible homology between sequences and potential similarities in gene function [43]. Hence, it is necessary for most users to find regions of similarity between biological sequences in gene information databases. GDS employs the free, open-source, and powerful Sequenceserver software for BLAST searches [44]. This interface of Sequenceserver is simple, user-friendly, and powerful (Figure 5). SequenceServer has a simple

interface, it performs BLAST and visually inspect BLAST results for biological interpretation. It uses simple algorithms to prevent potential errors during analysis and provides flexible text-based, visual outputs to support researchers' work efficiency. SequenceServer is a BLAST+ server for personal use with a clear and thoughtful design. It contains genomic sequences, CDS, and protein sequences of strawberries, and uses jstree to optimize BLAST to offer clear visualization of complicated results.



**Figure 5.** The BLAST tool integrated into GDS. (**a**) A user can enter genomic, PEP, or CDS sequences into the text box, then select the species name below; (**b**) the resulting alignment scores are ranked from high to low, and the details of each sequence alignment are given below the list of scores.

#### *3.10. Genomic Visualization Using JBrowse*

A genome browser is a software tool that can be deployed on the server side so that users can access online platforms. JBrowse is a fully featured genome browser that can visualize various types of genome-located data, located in a variety of different data stores, and interfacing to other client and server applications. We used JBrowse [45] built using HTML5 and JavaScript. It integrates and visualizes various existing genome data, including eight nuclear genomes and seven chloroplast genomes [46] so that users can visually browse and analyze the genome and various types of annotation data with strong scalability (Figure 6). In addition, the genome browser can support other types of data, such as repetitive sequences.

**Figure 6.** The JBrowse tool integrated into GDS for visualization of strawberry genomic details. (**a**) Gene visualization interface; (**b**) detailed data on individual genes.
