Overview of comparative genomic pipeline: Genomic Analysis for Illuminating Structured RNA (GAISR). Putative 5′-untranslated regions (5′-UTRs) of our gene of interest (rpsO) are identified within completed microbial genomes and clustered by their taxonomic group. CMfinder is used to identify potential conserved RNA structures within these sequence clusters . Following RNA structure identification, the candidate RNA structures are manually inspected and additional homologs are identified using Infernal 1.1 . The genomic context of putative homologs is assessed, and they are incorporated into the alignment using cmalign. The alignment is then typically manually inspected to identify potential pseudoknots or other regulatory features and the curation process may be repeated several times. Finally, transcriptomic data is sought to identify the transcription start site of the putative ncRNA.