Online plastome DNA-barcoding marker discovery

MarkerSeek Analyzer

Upload annotated GenBank plastomes to discover and rank DNA-barcoding markers. MarkerSeek aligns the sequences, scans nucleotide diversity, scores candidate regions, and designs in-silico primer pairs, returning publication-ready figures and tables.

  • Pi sliding-window analysis
  • Hotspot annotation
  • Candidate-marker scoring
  • Primer design & in-silico PCR
  • mVISTA-style similarity tracks
1
Upload plastomes Add annotated GenBank files from comparable plastomes.
2
Configure analysis Set Pi window, hotspot, similarity, and primer options.
3
Export results Get marker tables, primer pairs, and figures by job ID.

Input files

Upload 2-20 annotated GenBank files. Drag-and-drop is supported.

GenBank files

Accepted formats: .gb, .gbk, and .genbank. Selected files also fill the reference selector below.

Selected 0/20 files
Maximum 20 files. Use consistently annotated plastomes.

Analysis parameters

Core settings for the sliding-window Pi scan.

Defaults suit most plastomes; adjust for finer or smoother hotspots.

Hotspot labeling

Each gene or spacer is labeled once in the plot.

Top-percent for screening, top-N for a fixed panel, threshold for a set Pi cutoff.

Similarity plot

mVISTA-style identity tracks for non-reference samples.

Pick a reference after upload, or leave it to use the first sorted file.

Primer design

Optional primer3 design with in-silico PCR on the candidate markers.

Primer parameters

Uses conserved flanks, primer3, and in-silico PCR to check primer availability.

View existing results