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Evolutionary Genomics

Volume 855 of the series Methods in Molecular Biology pp 175-201

Date:

Gene Prediction

  • Tyler AliotoAffiliated withCentro Nacional de Análisis Genómico Email author 

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Abstract

Evolutionary genomics is a field that relies heavily upon comparing genomes, that is, the full complement of genes of one species with another. However, given a genome sequence and little else, as is now often the case, genes must first be found and annotated before downstream analyses can be done. Computational gene prediction techniques are brought to bear on the problem of constructing a genome annotation as manual annotation is extremely time-consuming and costly. This chapter reviews the methods by which the individual components of a typical gene structure are detected in genomic sequence and then discusses several popular statistical frameworks for integrated gene prediction on eukaryotic genome sequences.

Key words

Gene prediction Dynamic programming Hidden Markov model Conditional random field Coding statistics Coding potential Genome annotation Markov chain