Hello, I am Master student under molecular biology.
I want to find the Shine-Dalgarno sequence after performing a BLAST search in TargetRNA2. Could you please suggest a web tool to predict the Shine-Dalgarno sequence?
I would also like to know if there are any papers that discuss the minimum base pair distance between flanking genes required to categorize them as trans-acting or cis-acting.
Unfortunately, TargetRNA2 itself doesn't predict Shine-Dalgarno (SD) sequences. However, following a BLAST search on TargetRNA2, you can use several web tools to analyze the resulting sequence and predict the SD sequence:
1. RBSfinder: https://global.tamu.edu/isss/students/employment/cpt
This tool from the Center for Phage Technology (CPT) specifically focuses on Ribosome Binding Sites (RBS), which includes the SD sequence. You can paste your sequence from the BLAST result and choose to "Report best hits only" to get the most likely SD sequence.
2. BACTERIO.NET: https://www.bacterio.net/
This website offers various tools for analyzing bacterial sequences. It includes a "Shine/Dalgarno Sequence Finder" where you can paste your sequence and get potential SD motifs identified.
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