Computational Genomics

As was previously mentioned, an organism's genome contains a lot of repeating, noncoding regions of DNA in addition to the useful sequences that encode proteins. Thus, because only the coding regions encode proteins, it is useful to look at those, as they are the sequences that will have an effect on the physiology of the cell. In addition, even in the coding region of most organisms, there are sequences that are transcribed, but not translated into a functional protein called Introns. Recall that DNA is transcribed by RNA Polymerase into an mRNA transcript. Before leaving the nucleus, however, this mRNA transcript often goes through splicing to remove any Introns that exist in the mRNA sequence before being translated into a protein by Ribosomes. Therefore, it is difficult to determine what sequences are important simply by looking at the genome of an organism. Instead, we look at fully processed strands of mRNA after transcription and splicing. The mRNA is isolated from cells and a DNA transcript complementary to that mRNA strand is created, called a cDNA. This cDNA is generated through the use of a protein called Reverse Transcriptase, a protein found in retroviruses that invade cells. The process is shown in the following diagram: