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Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN

Part of the Methods in Molecular Biology book series (MIMB,volume 2242)

Abstract

Over the last 15 years, the costs of DNA sequencing have sharply fallen, effectively shifting the costs of DNA analysis from sequencing to bioinformatic curation and storage. A huge number of available DNA sequences (including genomes and metagenomes) resulted in the development of various tools for sequence annotation. While much effort has been invested into the development of automatic annotation pipelines, manual curation of their results is still necessary in order to obtain a reliable and strictly validated data. Unfortunately, due to its time-consuming nature, manual annotation is now rarely used.

In this chapter, a protocol for efficient manual annotation of prokaryotic DNA sequences using a novel bioinformatic tool—MAISEN (http://maisen.ddlemb.com), is presented. MAISEN is a free, web-based tool designed to accelerate manual annotation, by providing the user with simple interface and precomputed alignments for each predicted feature. It was designed to be available for every scientist, regardless of their bioinformatic proficiency.

Key words

  • Bacterial genomics
  • Functional annotation
  • Gene prediction
  • Genome annotation
  • Manual annotation
  • Next-generation sequencing

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Acknowledgments

This work was supported by the National Science Centre, Poland (grant number 2016/22/E/NZ8/00340).

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Correspondence to Lukasz Dziewit .

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Dziurzynski, M., Decewicz, P., Ciuchcinski, K., Gorecki, A., Dziewit, L. (2021). Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN. In: Mengoni, A., Bacci, G., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 2242. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1099-2_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1099-2_14

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  • Publisher Name: Humana, New York, NY

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