GeneSeekr

What does it do?

Use GeneSeekr to detect predefined or custom gene targets in FASTA-formatted files. GeneSeekr operates on assembled sequence data; use Sipprverse when the targets must be detected directly in raw, paired-end FASTQ reads.

GeneSeekr supports gene detection, selected typing analyses, and custom target databases. The supported analysis name must be supplied in the Redmine issue Description.

How do I use it?

Subject

In the Subject field, enter:

geneseekr

Spelling matters, but matching is not case-sensitive.

Description

The Description field must contain:

  1. an analysis declaration in the form analysis=requested_analysis;
  2. any additional field required by that analysis; and
  3. one SEQID per line.

Example structure:

analysis=resfinder
2026-SEQ-0001
2026-SEQ-0002

Supported analyses

  • gdcs — detects genomically dispersed conserved sequences in Escherichia, Listeria, Salmonella, and Vibrio. Also include organism=ORGANISM.
  • genesippr — uses a custom suite of genes derived from Bacillus, Campylobacter, Escherichia, Listeria, Salmonella, Staphylococcus, and Vibrio.
  • mlst — determines multilocus sequence type for Bacillus, Campylobacter, Escherichia, Listeria, Salmonella, Staphylococcus, and Vibrio. Also include organism=ORGANISM.
  • cgmlst — determines core-genome multilocus sequence type for Escherichia and Yersinia. Also include organism=ORGANISM.
  • resfinder — identifies acquired antimicrobial-resistance genes.
  • rmlst — determines ribosomal multilocus sequence type.
  • serosippr — calculates the serotype for Escherichia.
  • sixteens — determines the closest 16S match.
  • virulence — detects virulence genes.
  • custom — detects targets from a user-supplied FASTA file. This analysis requires an attachment.

GeneSeekr also provides analyses based on ICEberg databases from the ICEfinder publication:

  • all_ices — detects all included integrative and conjugative element targets.
  • aice — detects actinomycete integrative and conjugative element targets.
  • cime — detects cis-mobilizable element targets.
  • ime — detects integrative and mobilizable element targets.
  • t4ss — detects Type IV Secretion System targets.

The ICEberg databases are available from the ICEberg download page.

Attachments

Most standard analyses do not require an attachment.

For analysis=custom, attach a FASTA-formatted file containing the target sequences. The source documentation does not specify a required attachment filename or a Description parameter that refers to it; verify the attachment requirements with the current implementation if a custom request fails.

Optional parameters

blast

Selects the BLAST program.

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

GeneSeekr does not verify that the query and database molecule types are appropriate for the selected BLAST program. None of the standard analyses currently uses a protein database.

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
  • Example: evalue=1E-10

align

Controls whether reports include alignments.

  • Default: False
  • Example: align=True

unique

Controls whether only the best hit is reported when multiple hits occur at the same location in a contig.

  • Default: False
  • Example: unique=True

fasta

Controls whether the output includes FASTA files containing strain-specific target-sequence matches.

  • Default: False
  • Example: fasta=True

Examples

ResFinder request

analysis=resfinder
2026-SEQ-0001
2026-SEQ-0002

See issue 14470 for an example ResFinder request.

cgMLST request

analysis=cgmlst
organism=Escherichia
2026-SEQ-0001

See issue 27867 for an example cgMLST request.

Custom request

analysis=custom
2026-SEQ-0001

Attach the FASTA-formatted target file to the issue. See issue 14471 for an example custom request.

Interpreting results

When GeneSeekr finishes, it uploads:

geneseekr_output.zip

The archive contains the reports generated for the selected analysis. The supplied documentation does not define a single common report schema because the contents depend on the requested analysis. Interpret each report according to the selected analysis and its reported fields.

How long does it take?

Runtime depends on the selected analysis and the number of requested SEQIDs. As a general estimate, GeneSeekr takes approximately one minute per SEQID.

What can go wrong?

A requested SEQID is unavailable

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

Likely cause: GeneSeekr cannot locate the requested assembled sequence data.

What to do: Verify each SEQID and confirm that its FASTA-formatted assembly is available before submitting a corrected request.

The analysis is missing, misspelled, or unsupported

Symptom: The Redmine issue receives an error describing the requested analysis.

Likely cause: The Description does not include analysis=..., contains a spelling error, or requests an analysis that GeneSeekr does not support.

What to do: Choose one of the documented analysis names and submit a corrected request.

A custom target file is missing or unreadable

Symptom: The custom analysis cannot read or use its target database.

Likely cause: The FASTA-formatted target file was not attached or could not be read.

What to do: Attach a valid FASTA-formatted target file and submit a corrected analysis=custom request.

  • Sipprverse — use for predefined or custom target detection directly in raw, paired-end FASTQ reads.
  • KMA — use for its supported resistance and toxin analyses, or custom targets, in assemblies or raw reads.