Plasmid-Borne Identity

What does it do?

Use Plasmid-Borne Identity to search FASTA-formatted draft genome assemblies for user-supplied gene targets and predict whether each detected target is located on a plasmid or chromosome.

Plasmid-Borne Identity combines:

• GeneSeekr — searches assemblies for the attached target sequences;
• MOB-suite mob_recon — reconstructs and types predicted plasmids.

The combined report maps target-containing contigs to MOB-suite plasmid predictions. For additional MOB-suite output details, see the MOB-suite repository.

How do I use it?

Subject

In the Subject field, enter:

plasmid_borne_identity

Spelling matters, but matching is not case-sensitive.

Description

In the Description field, enter one SEQID per line. Optional GeneSeekr parameters can be placed on separate lines before the SEQIDs.

cutoff=80
2026-SEQ-0001
2026-SEQ-0002

Each requested SEQID must have a FASTA-formatted draft genome assembly available.

Attachments

Attach a FASTA-formatted file containing the gene targets to search for. The supplied documentation does not specify a required attachment filename or a Description parameter that refers to that filename.

Optional parameters

blast

Selects the BLAST program used by GeneSeekr.

• Default: blastn
• Accepted values: blastn, blastp, blastx, tblastn, tblastx
• Example: blast=tblastx

GeneSeekr and Plasmid-Borne Identity do not verify that the query and database molecule types are appropriate for the selected BLAST program.

cutoff

Sets the minimum cutoff for matches included in the report.

• Default: 70
• Example: cutoff=80

evalue

Sets the E-value cutoff.

• Default: 1E-05
• Examples: evalue=1E-10 or evalue=0.01

Examples

Nucleotide-target request

cutoff=80
2026-SEQ-0001
2026-SEQ-0002

Attach the FASTA-formatted target file. The default BLAST program is blastn.

Alternate BLAST program

blast=tblastx
evalue=1E-10
2026-SEQ-0001

Verify that the selected BLAST program is appropriate for both the attached targets and assembly database.

See issue 15644 for an example Plasmid-Borne Identity request.

Interpreting results

Plasmid-Borne Identity uploads five reports. {BLAST_PROGRAM} is replaced with the selected BLAST program, such as blastn.

geneseekr_{BLAST_PROGRAM}.xlsx

Reports the strain name and percentage-identity match for each query target.

geneseekr_{BLAST_PROGRAM}_detailed.csv

Reports detailed BLAST evidence for each target, including:

• strain name;
• percentage match;
• alignment length;
• subject length;
• E-value;
• positives;
• mismatches;
• gaps.

geneseekr_{BLAST_PROGRAM}.csv

Provides the GeneSeekr summary in CSV format.

mob_recon_summary.csv

Lists contigs predicted to be plasmid-derived. Contigs predicted to be chromosomal are omitted.

Important fields include:

• Location — the predicted plasmid name;
• Contig — the contig predicted to contain plasmid sequence.

One predicted plasmid can contain several contigs when it could not be circularized.

plasmid_borne_summary.csv

Combines detailed GeneSeekr target hits with MOB-suite plasmid predictions. It maps target-containing contigs to predicted plasmids and includes plasmid incompatibility types when available.

The Location field reports either:

• chromosome; or
• the name of a predicted plasmid.

This location is a computational prediction. Review the detailed BLAST evidence, assembly context, and MOB-suite reconstruction before drawing conclusions.

How long does it take?

GeneSeekr is fast, while MOB-suite is comparatively slower. Expect the combined analysis to take a few minutes per requested SEQID, depending on assembly size, target count, sample count, and service workload.

What can go wrong?

A requested SEQID is unavailable

Symptom: The Redmine issue receives a warning identifying unavailable sequences.

Likely cause: The automator cannot locate a draft genome assembly for the requested SEQID.

What to do: Verify each SEQID, confirm that its FASTA assembly is available, and submit a corrected request.

The target attachment is missing or invalid

Symptom: The automator cannot read or search the target sequences.

Likely cause: The target file was not attached or is not valid FASTA.

What to do: Attach a correctly formatted FASTA file containing the target sequences.

The BLAST program does not match the sequence types

Symptom: The analysis returns no useful hits or fails unexpectedly.

Likely cause: The selected BLAST program is incompatible with the attached query targets or nucleotide assembly database, for example blastp with nucleotide query and database sequences.

What to do: Verify the molecule type of the query targets and select the appropriate BLAST program. Use the default blastn for nucleotide targets searched against nucleotide assemblies.

A target has an uncertain predicted location

Symptom: A detected target cannot be confidently assigned to a predicted plasmid or chromosome.

Likely cause: Draft assemblies can fragment plasmids across contigs, and plasmid reconstruction is predictive.

What to do: Review geneseekr_{BLAST_PROGRAM}_detailed.csv, mob_recon_summary.csv, and the assembly context together.

Related automators

• GeneSeekr — searches FASTA-formatted files for predefined or custom targets without plasmid-location summarization.
• MobSuite — detects, reconstructs, and types predicted plasmids without requiring a user-supplied target set.
• AMRsummary — combines ResFinder acquired-AMR detection with MOB-suite plasmid-location predictions.