RUN THE ANALYSIS

Analysis description

Task name:

Input files*:

Accepted files: .gb, .gbk, .gbff, .fasta, .fa, .fsa, .fas, .fna, .txt

Alignment method*:

Automatic annotation:

At least one annotated file needs to be provided if automatic annotation is not selected

Extended Analysis (optional)

Select additional analyses to run on the reference sequence. Check a tool to enable it; expand the card to adjust its parameters.

PLSDB — BLASTn similarity search against the PLSDB plasmid database (v. 2024_05_31)

Min. Identity (%) BLAST hits below this % identity are discarded (default: 90)

E-value Maximum expect value for BLAST hits (default: 0.001)

Min. Coverage (%) Minimum query coverage for BLAST hits (default: 0)

AMRFinderPlus — Antimicrobial resistance gene identification (v. 2025-03-25.1)

Min. Coverage (0–1) Fraction of reference gene length that must be covered (default: 0.5)

Min. Identity (0-1 or -1) Minimum amino acid identity; -1 lets AMRFinderPlus choose automatically (default: −1)

PlasmidFinder — Plasmid replicon typing and incompatibility group classification (v. 2.2.0)

Min. Coverage (0–1) Minimum fraction of the replicon sequence covered (default: 0.4)

Min. Identity (0–1) Minimum nucleotide identity to the replicon database (default: 0.6)

pMLST — Plasmid multi-locus sequence typing via PubMLST schemes

Min. Coverage (%) Minimum allele coverage required for assignment (default: 40)

Min. Identity (%) Minimum allele identity required for assignment (default: 60)

Min. Score Minimum BLAST score for allele assignment (default: 30)

MOB-typer — Plasmid mobility and host range prediction (v. 3.1.8)

Min. Coverage (%) Minimum hit coverage for relaxase / oriT detection (default: 50)

Min. Identity (%) Minimum hit identity for relaxase / oriT detection (default: 60)

Primary Cluster Distance Mash distance threshold for primary cluster assignment (default: 0.1)

Bakta — Comprehensive bacterial genome and plasmid annotation (v. 6)

Topology Expected genome topology (default: circular)

Complete Genome Treat as a complete closed genome (default: yes)

eggNOG-mapper — Ortholog and functional annotation via the eggNOG database Coming soon

Automatic reference selection:

Please, select one file used as a reference in the table below.

Input fields with an * are required.