Geneticists use following two methods for sequencing the genomes: 1. Clone-by-clone Method 2. Shotgun Cloning.
Method # 1. Clone-by-Clone Method:
This method was the first to be developed. It begins with the construction of genomic libraries of restriction fragments covering all the genomic DNA (or genomic clones) of an organism. By using genetic markers, overlapping clones are assembled into genetic and physical maps encompassing the entire genome.
The nucleotide sequence is determined on a clone-by- clone basis until the entire genome is sequenced. The clone-by-clone method was chosen for the publically funded Human Genome project sponsored by the National Institutes of Health and Department of Energy (U.S.A).
Method # 2. Shotgun Cloning:
In this method, genomic libraries are prepared and randomly selected clones are sequenced until all clones in the library are analysed. Assembler software organises the nucleotide sequence information into a genome sequence.
This method, developed by Craig Venter and his colleagues at the Institute for Genome Research (TIGR), was used to sequence the genome of the bacterium Haemophilus influenzae in 1995, the first organism to have its genome completely sequenced.
After refining the method and using it to sequence the genomes of other prokaryotes, the shotgun method was used to sequence eukaryotic genomes, including Drosophila and humans. Using the shotgun method, venter and his colleagues started a privately funded human genome project. The project begun in September 1999 and sequencing was finished in June 2000.
By February 2001, when conclusions from the human draft sequence were published, complete sequences of genomes of 599 viruses and viroids, 205 naturally occurring plasmids, 185 organelles, 31 eubacteria, 7 archaea (bacteria), one fungus, two animals and one plant had become available.
Once the complete base sequence of a genome becomes available, scientists can begin to interpret the total information contained in the genome; this is termed as functional genomics. Thus, functional genomics involves determination of the functions of each protein encoded by the genome. The amino acid sequence of a protein may give a clue to its presumed function based on the similarity to already known proteins.