Whole genome sequencing era and genomics started in the 1970's when the first viral small genome was sequenced. The first bacterial genome was finished only a decade ago 1995 following larger eukaryotic genomes. The human genome draft version was published 2001. Most of these advances in analysis of the genome organization have been technology driven. During the years DNA sequencing has gone through several paradigm changes. The first was the invention of Sanger sequencing which enabled analysis of longer continuous DNA fragments which culminated to the development of capillary sequencing machines in 1998. These apparatuses eventually analyze 48-96 samples at the time with a throughput of about 500 000 bases /24 h.

The variability of the genes in the biosphere has surprised most of the scientist and the primary de novo sequencing is still one of the most efficient methods in describing biological entities. There is a need for even higher capacity of sequencing and lower prices. There are many important genomes that still have not been sequenced and the variability of strains of microbes or individuals in the case of humans completely unresolved because of the high price and too low speed of the current methodology. For solving these issues parallel sequencing has been in development by several companies like 454 Life Sciences and Solexa.

These technologies are 100-1000 times faster then the capillary platforms. Parallel to the interest of analyzing the genome organization interest for also analyzing the function of these genomes i.e. functional genomics has increased. DNA microarrays was published 1995 at the same year as the first big genome was published. DNA microarray technology makes is possible to analyze function of all the genes in a single assay. There are several competing platforms ranging from classical cDNA microarrays to in situ synthesized oligonucleotide arrays designed in silico. All the DNA sequencing and DNA microarray platforms still are just methods that can be used for many purposes entirely depending of the imagination and skills of the users.

One important unifying theme in genomics and functional genomics is the use of computational methods in analyzes of the results. Biology is eventually reaching to the stage when also modeling using bioinformatics tools will be amenable in larger number of projects. So far in most cases there has not been enough data to make system wide models that could be used for predictions.