Question

Imagine you identified what you believe to be a new, previously-unidentified spe- cies of bacterium. You therefore cultured the bacterium in the lab, purified RNA from the bacteria, made cDNA from the RNA, and obtained its sequence. What next step would you take to confirm whether this is, indeed, a novel species?

Answer 1

We have complete sequence information of cDNA. Now we will be using bioinformtic tolls to compare the sequence with already submitted database. If there is complete similarity of our sequence with any already submitted sequence information, then we can infer that the isolated bacteria is not novel. However, if there is not complete similarity of sequence then we can infer that we have indeed isolated a novel bacteria.

For this analysis we use a bioinformatic tool called Basic local allignment search tool.

We can go for16 rRNA similarity search by BLAST and see whether there is any difference or not..

16rRNA is a type of rRNA which makes part of 30S ribosomal subunit. Although this gene is extremely conserved owing to its role in bacterial protein synthesis. It aso contains 9-10 hypervariable regions of around 30-100 bp. We look for less conserved regions in this part for genus and species identification. Because these variations are extremely genus or species specific.