10 – Prediction of Human Gene Structure

An important problem in current molecular biology studies is gene identification. Due to recent progress in large-scale sequencing projects, gene identification programs have become widely used. The use of these programs can significantly simplify the analysis of newly sequenced DNA especially when applied in combination with experimental methods. The gene identification procedure is very complex owing to the structure of eukaryotic genes. The analysis of human genes cannot be considered merely as a linguistic analysis of the nucleotide string because the gene structure is made up of many other important features that include higher-order chromatin structure, the nonrandom nucleosome positioning along the DNA, the different features of the three-dimensional structure of the DNA (or RNA) and the torsional strain on the DNA induced by transcription. This chapter describes the most important aspects of gene structure prediction: functional sites in nucleotide sequence, functional regions in nucleotide sequences, protein-coding gene structure prediction, analysis of potential proteins coded by predicted genes, and RNA-coding gene structure prediction.

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