Long non-coding RNAs (lncRNAs) typically refer to non-protein coding RNAs that are longer than 200 nucleotides. Historically dismissed as junk DNA, over two decades of research have revealed that lncRNAs bind to other macromolecules (e.g., DNA, RNA, and/or proteins) to modulate signaling pathways and maintain organism viability. Their discovery has been significantly aided by the development of bioinformatics tools in recent years. However, the diversity of tools for lncRNA discovery and functional prediction can present a challenge for researchers, especially bench scientists and clinicians. This Perspective article aims to navigate the current landscape of bioinformatic tools suitable for both protein-coding and lncRNA genes. It aims to provide a guide for bench scientists and clinicians to select the appropriate tools for their research questions and experimental designs.