Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis

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    Abstract

    Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role.This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known. In this paper, we employ artificial neural networks to predict which AUG triplet in an mRNA sequence is the start codon. The trained networks correctly classified 88% of Arabidopsis and 85% of vertebrate AUG triplets. We find that our trained neural networks use a combination of local start codon context and global sequence information. Furthermore, analysis of false predictions shows that AUGs in frame with the actual start codon are more frequently selected than out-of-frame AUGs, suggesting that our nteworks use reading frame detection. A number of conflicts between neural network predictions and database annotations are analysed in detail, leading to identification of possible database errors.
    Original languageEnglish
    Title of host publicationProceedings Fifth International Conference on Intelligent Systems for Molecular Biology
    Place of PublicationMenlo Park, CA, USA
    PublisherAAAI Press
    Publication date1997
    Pages226-233
    Publication statusPublished - 1997
    Event5th International Conference on Intelligent Systems for Molecular Biology - Halkidiki, Greece
    Duration: 21 Jun 199726 Jun 1997
    Conference number: 5
    http://www.aaai.org/Library/ISMB/ismb97contents.php

    Conference

    Conference5th International Conference on Intelligent Systems for Molecular Biology
    Number5
    CountryGreece
    CityHalkidiki
    Period21/06/199726/06/1997
    Internet address

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