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Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes

: Donath, Alexander; Jühling, Frank; Al-Arab, Marwa; Bernhart, Stephan H.; Reinhardt, Franziska; Stadler, Peter F.; Middendorf, Martin; Bernt, Matthias

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Nucleic Acids Research 47 (2019), Nr.20, S.10543-10552
ISSN: 0305-1048
ISSN: 0301-5610
ISSN: 1362-4962
Zeitschriftenaufsatz, Elektronische Publikation
Fraunhofer IZI ()
Genomik; computational method; genome; Mitochondrium

With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.