Calculation of ratio non sinomic to sinonimic nucleotide substitution (dN/dS ratio)
Procedure contains three steps:
1 - calculation table of probability of substitution between two codons 2 - calculation of substitution between all sequences and referal sequence 3 - calculation of dN/dS ratio of each gene
Step one
Input table: codone_Cap_Low_tab_no-stop Output table dNdS.tab
Set of spetial instruction: dN_comb_tab
Run procedure (gawk should be installed): gawk -f calculation_dN_sites.awk codone_Cap_Low_tab dN_comb_tab > dNdS.tab
Step two
Input tables: dNdS.tab sequences.aln Output table: sequences.txt
Run procedure Parameters: name (ancessor genome) name_ref (referal genome) gawk -f dNdS_simple_cor.awk name=Ng87 name_ref=Ng87 dNdS.tab sequences.aln > sequences_dNdS_ind.tab
Step three
Input: table of substitution of each pair of genes (with referal genome) Output: dN/dS table
Run of procedure gawk -f dNdS_dist_gene_max.awk sequences_dNdS.txt > sequences_dNdS.tab