StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence

Gemayel, K.; Lomsadze, A.; Borodovsky, M.

doi:10.1101/2020.10.25.352625

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bioRxiv · 10.1101/2020.10.25.352625

StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence

Gemayel, K.·Lomsadze, A.·Borodovsky, M.

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Abstract

Algorithms of ab initio gene finding were shown to make sufficiently accurate predictions in prokaryotic genomes. Nonetheless, for up to 15-25% of genes per genome the gene start predictions might differ even when made by the supposedly most accurate tools. To address this discrepancy, we have introduced StartLink+, an approach combining ab initio and multiple sequence alignment based methods. StartLink+ makes predictions for a majority of genes per genome (73% on average); in tests on sets of genes with experimentally verified starts the StartLink+ accuracy was shown to be 98-99%. When StartLink+ predictions made for a large set of prokaryotic genomes were compared with the database annotations we observed that on average the gene start annotations deviated from the predictions for ~5% of genes in AT-rich genomes and for 10-15% of genes in GC-rich genomes.

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Gemayel, K., Lomsadze, A., Borodovsky, M.. 2020-10-26. StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence. https://doi.org/10.1101/2020.10.25.352625

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