Bioinformatic Tools

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)
DOI
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 …
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 …

SigMa
SigMa was designed for iterative prophage identification in bacterial genomes. It is meant to allow the incorporation of validated …
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
DOI
Literature-based, manually-curated database of PCR primers for the detection of antibiotic resistance genes in various environments
Adrian Gorecki, Przemyslaw Decewicz, Mikolaj Dziurzynski, Anna Janeczko, Lukasz Drewniak, Lukasz Dziewit
Water Research, 161, 211-221 (2019)
DOI
Literature-based, manually-curated database of PCR primers
A literature-based, manually-curated database of PCR primers for the detection of antibiotic resistance genes is comprised of hundreds …
DOI
Alphaproteobacteria (pro)phages Database
This projects aims to construct interactive website database for all known and publicly available active phages and manually verified …
Phages Prophages Sinorhizobium phages Paracoccus prophages
Stress response genes database
A manually curated database of stress response genes was created to annotate genes of plasmid DNA extracted from metaplasmidomes from …