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_36
Snippet: We computed alignment powers with R-scape 38 to assess the potential for using SARSr-MSA-1 for covariation analysis. We generated Stockholm alignment files with biopython 39 for windows of 120 nucleotides each sliding by 40 nucleotides. For each window, we ran R-scape with the -fold flag to predict new structures, obtaining estimates for the power of each base pair in the predicted structure (here, power is the expected sensitivity for detecting .....
Document: We computed alignment powers with R-scape 38 to assess the potential for using SARSr-MSA-1 for covariation analysis. We generated Stockholm alignment files with biopython 39 for windows of 120 nucleotides each sliding by 40 nucleotides. For each window, we ran R-scape with the -fold flag to predict new structures, obtaining estimates for the power of each base pair in the predicted structure (here, power is the expected sensitivity for detecting base pairs given the number of substitutions in the alignment at that base pair). We then averaged across base pairs in each structure to obtain the alignment power as described in Rivas, et al., 22 noting that all windows' alignment powers fell below the 0.10 threshold used by Rivas, et al. 22 to distinguish low-power from high-power alignments.
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