Markers and primers

The marker registry lists the genetic markers (such as COI-5P, rbcL, matK and ITS) that a sequence can be recorded against. The primer registry lists the PCR primers used to amplify them. Both live under Platform Management → Controlled Terms, on the Markers and Primers pages. You maintain them when a laboratory starts using a marker or primer the platform does not know, when an entry is wrong, or when two entries turn out to describe the same thing.

How the registries are used

The platform reads the two registries in several places, which is why an entry has to be right before data arrives:

• Sequence uploads. The marker pick-list on the Sequences upload dialog is built from the marker registry, and the record store accepts a sequence only for a marker code it can resolve. See Uploading sequences.
• Stop-codon checks. During sequence ingest, the stop-codon check runs only on markers flagged Protein Coding, and the marker's Genome (nuclear or mitochondrial) decides which translation table is used together with the record's taxonomy. A marker without the flag is never checked. See The two ingest jobs.
• Analysis forms. The marker field on each analysis form offers the registry's codes.
• Enrich record. The marker and primer pick-lists on the Enrich form come from the registries.
• Specimen uploads. Primer names or codes in a batch spreadsheet are resolved to the primer registry during ingest, using a copy of the registry that is exported each night.
• The Primers page. Any signed-in user can open Primers → View All Primers, select primers and download them as a FASTA file with the FASTA button. The same page lets any user register a new primer, which is live at once. The administrative page is the only place where a primer can be edited, deleted or merged.

Markers

To add a marker, choose Add Marker, fill in at least the code, and Save Changes. A code that already exists is refused. To change an entry, open it, choose Edit Marker and save. Editing a marker changes what every record that references it reports, because records store a link to the entry rather than its text.

Primers

A primer entry holds Code (required and unique), Name, Direction (F or R), Nucleotide Sequence in IUPAC letters, Alias, Namespace, Taxon Focus, the Marker it amplifies, the Cocktail and Public flags, a Reference, a Note, and the Verbatim Code and Verbatim Nucleotide as they appeared in the source. Add Primer and Edit Primer work the same way as for markers.

Merging two entries

There is no plain delete. Removing a marker or primer always means merging it into another one, so that nothing which referenced the old entry is left pointing at nothing.

1. Open the entry and choose Delete Marker (or Delete Primer).
2. Pick the surviving entry under Replace with.
3. Choose Delete & Reassign.

For a marker, every reference to the old entry is re-pointed to the replacement before the old row is removed: sequences, primers that name the marker, the marker links on projects, PCR records and the public records registry. Records lose nothing; they now report the replacement marker. For a primer, the forward and reverse primer references on PCR records are re-pointed, then the old primer is removed.

Pick a replacement that describes the same gene region. The merge cannot be undone from the interface.

Good to know

• A marker merge does not update the per-record feature summary, the row behind the icons in the records table and the compliance report. Those rows keep the old marker code.
• Changing a marker's Protein Coding flag or Genome affects sequences uploaded afterwards. Sequences already loaded are not re-checked for stop codons.
• Because any user can register a primer from the Primers page, expect to tidy near-duplicates here. Registration refuses a duplicate code or sequence, nothing more.
• Batch specimen uploads resolve primers against a registry copy exported nightly, so a primer added today is matched by spreadsheets processed from tomorrow. The sequence upload dialog and the Enrich form read the live list.

Related

• Uploading sequences
• The two ingest jobs
• Controlled vocabularies and validation rules
• The administrator role