Motivation

Working with environmental isolates, often from extreme environments (e.g. Arctic, Antarctic or highly polluted post-industrial sites) has taught us that automatic annotation pipelines are often not sufficient to correctly characterize their genomes. Moreover, mobile genetic elements of these strains are often incorrectly indicated by existing tools and therefore, they require manual verification.

In order to make that process more time-efficient, replicable, and to make manually curated annotations and automatic predictions reusable, we present a web-based application - MAISEN, that provides users with an interface to view, modify and reuse annotations of genomic sequences. MAISEN incorporates a set of bioinformatic tools and databases to help Users maintain their annotated sequences. It provides them precomputed search results so that they could focus on analysing results of those searches and making decisions as to what function a certain genomic feature (e.g. protein or genome segment) should have assigned.

The current version - MAISEN 2, compared to the first version resigns from providing automatic annotation on behalf of well established bioinformatic tools and pipelines such as NCBI Prokaryotic Genome Annotation Pipeline (PGAP), RAST at BV-BRC or local tools such as Bakta, Prokka or Pharokka specifically for phage genomes. Instead, it focuses on providing Users their own worskpace where they can manage their sequences and annotations. Therefore, we currently accept only GenBank files as input with complete annotations. Moreover, as one of the main novelties is the introduction of GenBank-like User Collection Qualifiers that allow Users to create their own qualifiers and use them to annotate their sequences. These can be used to create custom genomic feature qualifiers and later on, to create custom Collections of genomic features. These can be either private or public and shared with other Users.

Databases
Tools
Feedback

If you have any questions, comments or suggestions, please contact us at maisen@ddlemb.com or p.decewicz@uw.edu.pl.

Citing

If you use MAISEN in your research please cite the following article, as well as databases and software used during your analysis: Dziurzynski M, Decewicz P, Ciuchcinski K, Gorecki A, Dziewit L. Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN. Methods Mol Biol. 2021;2242:221-229. doi: 10.1007/978-1-0716-1099-2_14. PMID: 33961227.

Authors

Przemyslaw Decewicz, PhD
Karol Ciuchcinski, MSc

Department of Environmental Microbiology and Biotechnology
Institute of Microbiology, Faculty of Biology, University of Warsaw
website: http://ddlemb.com/

Funding

This work was supported by the Polish National Agency for Academic Exchange Bekker Programme Fellowship [grant no. BPN/BEK/2021/1/00416] and the National Science Centre, Poland [grant nos. 2016/23/B/NZ8/01638, 2018/29/N/NZ8/00228].