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Computational Methods for Ab Initio and Comparative Gene Finding

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Data Mining Techniques for the Life Sciences

Part of the book series: Methods in Molecular Biology ((MIMB,volume 609))

Abstract

High-throughput DNA sequencing is increasing the amount of public complete genomes even though a precise gene catalogue for each organism is not yet available. In this context, computational gene finders play a key role in producing a first and cost-effective annotation. Nowadays a compilation of gene prediction tools has been made available to the scientific community and, despite the high number, they can be divided into two main categories: (1) ab initio and (2) evidence based. In the following, we will provide an overview of main methodologies to predict correct exon–intron structures of eukaryotic genes falling in such categories. We will take into account also new strategies that commonly refine ab initio predictions employing comparative genomics or other evidence such as expression data. Finally, we will briefly introduce metrics to in house evaluation of gene predictions in terms of sensitivity and specificity at nucleotide, exon, and gene levels as well.

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Acknowledgments

This work was supported by the projects VIGNA (Ministero Politiche Agrigole e Forestali), LIBI – Laboratorio Internazionale di Bioinformatica (Fondo Italiano Ricerca di Base, Ministero dell’ Università e della Ricerca), Laboratorio per la Bioinformatica e la Biodiversità Molecolare (Ministero dell’Università e della Ricerca), Telethon, and AIRC.

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Authors and Affiliations

  1. Dipartimento di Biochimica e Biologia Molecolare “E. Quagliariello”, University of Bari, Bari, Italy

    Ernesto Picardi & Graziano Pesole

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  1. Ernesto Picardi
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  2. Graziano Pesole
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Editors and Affiliations

  1. Max F. Perutz Laboratories GmbH, Universität Wien, Dr. Bohr-Gasse 9, Wien, 1030, Austria

    Oliviero Carugo

  2. Research (A*STAR), Agency for Science & Technology, Biopolis Street 30, Singapore, 138671, Singapore

    Frank Eisenhaber

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Picardi, E., Pesole, G. (2010). Computational Methods for Ab Initio and Comparative Gene Finding. In: Carugo, O., Eisenhaber, F. (eds) Data Mining Techniques for the Life Sciences. Methods in Molecular Biology, vol 609. Humana Press. https://doi.org/10.1007/978-1-60327-241-4_16

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  • DOI: https://doi.org/10.1007/978-1-60327-241-4_16

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-240-7

  • Online ISBN: 978-1-60327-241-4

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