On the Accuracy of the 16S-rRNA Gene Conserved Regions

Graph search and variable neighborhood search for finding constrained longest common subsequences in artificial and real gene sequences

“…Established contigs were used for evaluation of the conservation degree of the conserved regions separating the hypervariable regions of the 16S rRNA gene in [36]. More precisely, for every contig and every gene from the considered databases, the longest common subsequence is calculated.…”

“…For the purpose of our tests, we adapted a set of 16S rRNA gene sequences and utilized a set of primer contigs from 16S rRNA gene as patterns generating a CLCS problem. Both types of sequences, 16S rRNA gene sequences and primer contigs sequences, contain some of the degenerate bases R, Y, M, K, S, W, H, D, B, V, and N. These degenerate bases can be replaced with corresponding amino acids [36]. For each of them exist two, three, or four possible amino acids.…”

“…More precisely, we made the following replacements: R with A, Y with C, M with A, K with G, S with G, W with A, H with A, D with G, B with G, V with G and N with A. More about these replacements can be found in [36].…”