Author: Ramya Rangan; Ivan N. Zheludev; Rhiju Das
Title: RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses Document date: 2020_3_28
ID: kjeqdse5_34
Snippet: RNAz 21 structures were predicted in windows of the SARS-CoV-2 genome using the SARSr-MSA-1 alignment. We used rnazWindow.pl to compile alignment windows across SARSr-MSA-1 with at least 4 sequences in each window, using a window size of 120 nucleotides sliding by 40 nucleotides, and using default settings otherwise. RNAz hits were computed at the P>0.5 threshold for the forward strand with z-scores computed without a shuffled sequence background.....
Document: RNAz 21 structures were predicted in windows of the SARS-CoV-2 genome using the SARSr-MSA-1 alignment. We used rnazWindow.pl to compile alignment windows across SARSr-MSA-1 with at least 4 sequences in each window, using a window size of 120 nucleotides sliding by 40 nucleotides, and using default settings otherwise. RNAz hits were computed at the P>0.5 threshold for the forward strand with z-scores computed without a shuffled sequence background for efficiency, using the --no-shuffle flag. The resulting RNAz structured windows were then clustered with rnazCluster.pl, filtered with rnazFilter.pl at a P>0.9 threshold, and sorted with rnazSort.pl.
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