assorted flu utils and analyses
So far just a couple of analyses:
-
Generate all nucleotide substitutions in the H1N1 genome and analyze delta-KD for various nt-substitution types. Example: What's average dKD for the A->G substitution?. Has something to do with the mutational bias observed under Favipiravir (mutagen) treatment.
-
Pandemic H1N1 (pH1N1), pulled from fludb.org, analysed, cleaned, then coding sequences are identified for each sequence (along with some extra filtering), and the final alignment is formed. This alignemnt is needed for further SNP patterns vs RNA-structure pattern analysis.
-
RNA structure & loci of interest association analysis. Series of heatmaps to plot for different features of RNA-loci association: is loci np-bound, paired, in a hairpin, etc. For all these features caluclate observed association-'probability' and the expected ones.