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Analysing a genome - o Gene prediction through similarity...

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Analysing a genome So, what does one do with a complete genome? After all, a sequenced genome consists only of so many bases in a defined order. Analysis is obviously necessary in order to obtain biologically interesting information. The analysis of a genome covers many different aspects. Here follows a list of the most common ones, but it is clear that entirely novel ways of analysing a complete genome can be invented. The potential for interesting discoveries in the complete genomes is great; we have probably just scratched the surface so far. Define the location of genes (coding sequences, regulatory regions): gene prediction (identification). o Gene prediction ab initio using software based on rules and patterns. Find Open Reading Frames (ORFs), with some additional criteria. Fairly simple for bacteria, very difficult for eukaryotes. o Gene identification through alignment with know proteins and EST sequences.
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Unformatted text preview: o Gene prediction through similarity with proteins or ESTs in other organisms. o Gene prediction through comparison with other genomes; conserved regions may be coding or regulatory regions. Synteny. • Annotation of the genes: Identify with known genes, similarity with genes in other organisms. Essentially: labelling the gene. • Functional classification. Broad groups of functional characterization, such as 'ribosomal proteins', 'nucleotide metabolism', 'signal transduction'. • Metabolic pathways. o Are any common pathways missing? o Are there 'gaps' (missing enzymes) in some pathways? o Compare identified pathways with the life style of the organism. • Evolutionary history o Internal genome duplications can sometimes be detected. o Gene decay can sometimes be characterized: genes that are on their 'way out' after duplication, or because the life style of the organism has changed....
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