RNA motifs, RNA structure, and motif context analyzed by RNAanalyzer3.

RNAanalyzer3 ("RNA analyzer cubic"; https://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de) substitutes the frequently consulted current RNAanalyzer webserver (https://rnaanalyzer-old.bioapps.biozentrum.uni-wuerzburg.de). RNAanalyzer3 is free/open via the secure HTTPS protocol, with example data, help and tutorial, web-link to results, and rich data output. We combine a general detailed structure analysis with motif analyses. It accepts either a single plain-text nucleotide sequence or batch submission in FASTA format, which can be pasted or uploaded as a FASTA file. Our tool (i) has up-to-date software and operating systems, (ii) combines diverse RNA motif analyses with RNA structure prediction, (iii) puts found motifs into structural context, and (iv) offers dedicated tools for probing RNA-protein binding interactions. RNAanalyzer3 links motif searches to Rfam and miRNA search to miRbase. It focuses on structural features first, looks for stem-loops, hairpins, and specific enrichment regions such as stem-GG pairs, plus AU-rich regions with their locations for easier identification, while providing structural context and interactive RNA structure visualization. A tabulated overview shows all RNA features including structure details, coding potential, untranslated regions (UTRs, including Shine-Dalgarno sequences, Kozak sequences, and polyadenylation signals), transfer RNA (tRNA), microRNA (miRNA), long noncoding RNA (lncRNA), trans-splicing motifs, iron response elements (IRE), riboswitches, small nuclear ribonucleoprotein (snRNP) motifs, and spliceosomal Sm-sites.