From genome sequences to function (annotation)

For any organism, once whole genome sequence becomes available, the next step in genomics research is to assign meaning or function to different regions of the genome. This is sometimes described as annotation of genomic sequences, thus ushering in the ‘Post genomic’ or ‘functional genomics’ era. This can be done in a variety of ways, the simplest being the identification pen reading frames (ORFs) with the help of locating initiation and termination codons followed by  comparison of these ORFs with the sequence of known function available in the databases.

The function of a DNA sequence means different things to people working in different areas of biology. For instance, a computational biologist may like to know only the class of substance that is encoded (e.g. a kinase), a biochemist may like to know intracellular localization, a geneticist may like to like to know the pathway it affects, a physiologist may like to know the organ it affects, and so on. Several approaches that are being used for understanding genome-wide functions include the following: (i) comparative genomic study to identify genes that are conserved enbloc in a variety of prokaryotes (guilt by association approach) (ii) study of the expression of all RNAs using oligonucleotides or cDNA arrays followed by further experimentation using a reductionist approach; (iii) a parallel development in the field of proteomics.