The analysis of a single gene sequence is done by establishing similarity with other known genes, determining phylogenetic trees and evolutionary relationships; identifying well-defined domains in the sequence, identifying physical properties, binding sites and modification sites comprising of the protein sequence features.
For analysis of complete genomes and to determine which gene families are present in the protein and which are not present, several techniques such as location of genes on the chromosomes, correlation with function or evolution, expansion of duplication of gene families, identification of missing enzymes, and presence or absence of biochemical pathways are considered. Large scale events that have affected the evolution of organisms are also studied for genome analysis.
When genes or genomes are analyzed with respect to functional data the techniques used are expression analysis, micro array data, mRNA concentration measurements, protein concentration measurements, proteomics, and covalent modifications. For analysis of gene and genomes from a functional perspective, comparative analyses of biochemical pathways are made along with deletion or mutant genotypes vs. phenotypes and identification of essential genes, or genes involved in specific processes in structure and functions of the organisms.
Analysis of protein structure and functions are done with the help of computer simulations which are used as tools to investigate protein structure and dynamics under a wide variety of conditions. ...