Gene prediction

In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced.

In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms. Statistical analysis of the rates of homologous recombination of several different genes could determine their order on a certain chromosome, and information from many such experiments could be combined to create a genetic map specifying the rough location of known genes relative to each other. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computational problem.

Determining that a sequence is functional should be distinguished from determining the function of the gene or its product. Predicting the function of a gene and confirming that the gene prediction is accurate still demands in vivo experimentation^[1] through gene knockout and other assays, although frontiers of bioinformatics research ^[2] are making it increasingly possible to predict the function of a gene based on its sequence alone.

Gene prediction is one of the key steps in genome annotation, following sequence assembly, the filtering of non-coding regions and repeat masking.^[3]

Gene prediction is closely related to the so-called 'target search problem' investigating how DNA-binding proteins (transcription factors) locate specific binding sites within the genome.^[4][5] Many aspects of structural gene prediction are based on current understanding of underlying biochemical processes in the cell such as gene transcription, translation, protein–protein interactions and regulation processes, which are subject of active research in the various omics fields such as transcriptomics, proteomics, metabolomics, and more generally structural and functional genomics.