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How is the RBS spacer distance counted?
Link to this post | posted today, 21:07 | |
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How is the RBS spacer distance counted in DNA Master? At which position in the Shine-Dalgarno sequence does the count start? I see an indication for how the spacer distance is calculated in the Bioinformatics Guide that doesn't seem to match what I see in DNA Master. The article indicates it counts from the G (in brackets): TAAGGAG[G]TA. (This raised other questions for me since I don’t think that G is even in the consensus sequence in the Kibler6 scoring matrix. See attachment.). https://seaphagesbioinformatics.helpdocsonline.com/article-24 When I look at output of SD sequences identified in DNA Master, it looks to me like the count starts earlier in the consensus sequence (where I have inserted the "|" symbol): TAA|GGAGGTA Examples of sequence upstream of annotated starts: • TCAAGACAA|GGAGACAAGCGCC spacer distance 13. Gene 12 Andre, z-score 3.17. • ACCCGCTCACAGAGA|GGAAGAA spacer distance 7. Gene 19 Andre, z-score 3.15. • AAACCATGAAA|GGAAGGCCATC spacer distance 11. Gene 8, MulchExplorer, Z-score 3.22. I'm also curious whether the spacer distances you see in the Karlin Medium Shine-Dalgarno spacer matrix in the local settings of DNA Master are counted the same way as the spacer distances in the "Choose ORF start" RBS window (accessed through the Frames window in DNA Master). A few extra questions on RBS sequence analysis in DNA Master: Also, does the z-score in the RBS table take into account the spacer distance? I know the final score does and that the raw score does not, but I'm not sure about the z-score. Are there any good resources that could help students interpret these scores and connect these scores to some basic concepts in statistics? Looking at this made me realize I also have some questions about the Kibler6 consensus sequence matrix and what it is looking for. The consensus sequence highlighted in the Kibler6 matrix cuts off earlier than I would have expected given other descriptions of the SD consensus sequences. See attached document for screenshots and descriptions of what I've been trying to sort out. Thank you so much! (Edit: seems my word doc attachment won't upload) |