Plastome DNA-barcoding marker discovery

Welcome to MarkerSeek

MarkerSeek finds hypervariable plastome regions, scores them transparently, and designs in-silico primer pairs for 2,112 genera.

Try: Salvia Allium Solanum Quercus Camellia
Browse all 2,112 genera Analyze your own plastomes
2,112
Genera
16,822
Plastomes
37,628
Primer-ready markers
192,055
Primer pairs
348
Families
128
Orders
Pipeline

From plastomes to publication-ready markers

One reproducible workflow handles alignment, diversity scanning, scoring, and primer design — all downloadable.

1 Upload GenBank →
2 Align & scan π →
3 Score regions →
4 Design primers
MarkerSeek workflow: GenBank inputs, plastome alignment, nucleotide diversity and similarity plots, MarkerSeek score, genus database, and primer design.
The MarkerSeek pipeline and resources.
Capabilities

Reproducible plastome marker discovery

From annotated GenBank inputs to ranked candidate regions and primer-ready markers, every result is traceable, comparable, and downloadable.

GenBank input

Upload annotated plastome GenBank files (.gb/.gbk/.genbank). MarkerSeek aligns them with MAFFT into a clean multiple alignment.

Nucleotide diversity (π)

A sliding-window π scan across the whole plastome pinpoints hypervariable hotspots gene-by-gene and spacer-by-spacer.

mVISTA similarity

Reference-anchored identity tracks visualise conservation and divergence across every sample at a glance.

MarkerSeek score

Ten weighted diagnostics — diversity, resolution, barcoding gap, conserved flanks and more — rank every region 0–100.

Primer design

primer3 designs pairs in conserved flanks, then in-silico PCR estimates cross-species amplification success.

Pre-computed catalogue

Browse ready-made markers for thousands of genera — no upload needed. Search, filter, and download tables and figures.

Download

Download MarkerSeek database

Download catalogue-wide tables for all indexed genera, or open the example output package for your own plastome workflow.

All genera catalogue Download genus-level taxonomy, plastome counts, marker counts, and primer-ready marker counts. All candidate markers Download catalogue-wide candidate marker features with genus, family, order, and species-count columns. All primer pairs Download catalogue-wide primer-pair TSV records with amplicon-size ranges. Example output View figures, marker details, downloadable files, and result layout.