Figure 1 summarizes the main avenues of research. Since the early work of Fickett, in which methods were developed to distinguish coding from noncoding regions, a plethora of strategies have been explored and many methods developed to elucidate the exonic structure of genes in eukaryotic genomes. The gene-finding problem has consequently attracted wide attention within the field of bioinformatics. Indeed, the vast majority of the biology of a genome is initially inferred from the set of proteins that genome is predicted to encode. ĭespite all these caveats, delineating the set of protein-coding genes is invariably the first step taken after completing the DNA sequencing of a genome. This is not a trivial task, as illustrated by the fact that many years after the first drafts of the human genome sequence became available, uncertainty remains regarding the exact number of protein-coding genes, a number that might actually vary between individuals - and even between cells within the same individual - as extensive structural variation has been reported in the human genome. The delineation of the complete set of protein-coding genes and their alternative splice forms is, therefore, essential to the task of translating the information in the sequence of the genome into biologically relevant knowledge. While the importance of noncoding RNAs has come to the fore over the past ten years, proteins are still assumed to be the main functional and structural players in the cell. According to the standard model, the majority of RNA sequences originate from protein-coding genes that is, they are processed into messenger RNAs (mRNAs) which, after their export to the cytosol, are translated into proteins. The unfolding of these instructions is initiated by the transcription of the DNA into RNA sequences. The genome sequence is an organism's blueprint: the set of instructions dictating its biological traits.
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