Bioinformatic Tools

Plant–pollinator interactions and floral and nectar traits shape the diversity of the nectar mycobiome
Kamil Kislo, Marcin Mazurkiewicz, Bartlomiej Starzynski, Marcin Zych, Mikolaj Wolacewicz, Andrzej Bajguz, Magdalena Chmur, Katarzyna Roguz
Scientific Reports, 16: 13253 (2026)
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Computational pipeline for sustainable enzyme discovery through (re)use of metagenomic data
Karol Ciuchcinski, Anna-Karina Kaczorowska, Daria Biernacka, Sebastian Dorawa, Tadeusz Kaczorowski, Younginn Park, Karol Piekarski, Michal Stanowski, Takao Ishikawa, Runar Stokke, Ida Helene Steen, Lukasz Dziewit
Journal of Environmental Management, 382, 125381 (2025)
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MAISEN
MAISEN is a web tool dedicated to annotating bacterial and archaeal nucleotide sequences. It allows you to browse structural and …
Mikolaj Dziurzynski, Przemyslaw Decewicz, Karol Ciuchcinski, Adrian Gorecki, Lukasz Dziewit
MAISEN
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Vijini Mallawaarachchi, Michael J. Roach, Przemyslaw Decewicz, Bhavya Papudeshi, Sarah K. Giles, Susanna R. Grigson, George Bouras, Ryan D. Hesse, Laura K. Inglis, Abbey L. K. Hutton, Elizabeth A. Dinsdale, Robert A. Edwards
Bioinformatics, 39, 10, btad586 (2023)
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Plasmids of psychrotolerant bacteria
Sequences of plasmids from cold-active bacteria from Nucleotide database (NCBI) in fasta format.
LCPDb-MGE – database of PCR primers for identification of mobile genetic elements
The database of PCR primers was based on a systematic literature review of articles in PubMed. It Contains information about starter …
Excel spreadsheet Spreadsheet as PDF
Mobile genetic elements of psychrotolerant prokaryotes

Here, we present a set of manually curated datasets of prokaryotic psychrotolerant genomes, their plasmids and metagenomes from cold …

Psychrotolerant prokaryotes metagenomes from cold environments PsychroPlasDb Plasmids: annotated GenBank files Plasmids: contigs Plasmids: proteins Phages: annotated GenBank files Phages: contigs/genomes Phages: proteins Proteins: MOBs Proteins: REPs Proteins: TerLs Proteins: MCPs Proteins: TNPs
SigMa
SigMa was designed for iterative prophage identification in bacterial genomes. It is meant to allow the incorporation of validated …
Development of the LCPDb-MET database facilitating selection of PCR primers for the detection of metal metabolism and resistance genes in bacteria
Mikolaj Dziurzynski, Adrian Gorecki, Przemyslaw Decewicz, Karol Ciuchcinski, Maria Dabrowska, Lukasz Dziewit
Ecological Indicators, 145, 109606 (2022)
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Simple, reliable, and time-efficient manual annotation of bacterial genomes with MAISEN
In: Methods in Molecular Biology: Bacterial Pangenomics, second edition
Edited by: A. Mengoni, G. Bacci, M. Fondi
Springer Protocols/Humana Press, USA, 2021, pp. 221-229
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