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Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models |
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| Authors: | Stephan Waack Oliver Keller Roman Asper Thomas Brodag Carsten Damm Wolfgang Florian Fricke Katharina Surovcik Peter Meinicke Rainer Merkl |
| Institution: | 1. Institut für Informatik, Universit?t G?ttingen, Lotzestr. 16–18, 37083, G?ttingen, Germany 2. Institut für Numerische und Angewandte Mathematik, Universit?t G?ttingen, Lotzestr. 16–18, 37083, G?ttingen, Germany 3. G?ttingen Genomics Laboratory, Universit?t G?ttingen, Grisebachstr. 8, 37077, G?ttingen, Germany 4. Institut für Mikrobiologie und Genetik, Universit?t G?ttingen, Goldschmidtstr. 1, 37077, G?ttingen, Germany 5. Institut für Biophysik und Physikalische Biochemie, Universit?t Regensburg, Universit?tsstr. 31, 93053, Regensburg, Germany |
| Abstract: | BackgroundHorizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands. |
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