MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

• MARS is a comprehensive RNA sequence database, 20-fold larger than NCBI's nt database and 60-fold larger than RNAcentral, integrating multiple sources including RNAcentral, MG-RAST, GWH, and MGnify. • The new split–search strategy in RNAcmap3 substantially improves homology search accuracy and sensitivity compared to existing state-of-the-art techniques. • MARS-based MSAs are more accurate and sensitive than manually curated Rfam MSAs for the majority of structured RNAs, enhancing structural and functional inference. • MARS and RNAcmap3 are publicly accessible, providing a valuable resource for RNA research and RNA language model development.