OpenCloning / OpenCloning/OpenCloning_frontend

Primer detailed information

Open
#429 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

help wanted
Dominant language
JavaScript
Stars
4
Forks
10
Avg merge
11d 9h
Merged PRs (30d)
3

Description

It's been a recurrent request to have some details about primer properties. I have a preliminary working version that shows minimal information in the primer table, and more info when clicking in the info icon

Table info

Image

The table looks like this and shows minimal information.

  • If a primer is not used for PCR or Oligonucleotide hybridization (bottom example), it shows values for the whole primer.
  • If primers are used for a PCR or Oligonucleotide hybridization (the four first rows in this example), it shows the value for the annealed part first, and then the value for the whole primer in parenthesis. For instance, for the first primer vector_fwd, length being 19 (36) means that the primer anneals with 19 bases, and has length 36. Then 50.2 (65.1) means that the Tm for the bound part is 50.2 and for the whole primer it's 65.1.
  • If a primer is used in several PCRs (probably edge-case), the first one is used.

Extra info

Then if you click on the info icon, you open a dialog with more detailed information (obtained from primer3). For the PCRs in which the primer is involved (highlighted in green), it shows values for both primers and difference of Tm between them.

Image

Icon warning

It would be good to come up with a set of parameters that would trigger warnings (show an alert triangle instead of a gray circle in the table as above). I don't really know what sensible values should be used for this. Also, the problematic rows in the extra info table could be highlighted in yellow / red depending how severe the problem is. For instance ( <30% / >70% GC yellow, 20/80 red).

Happy to take suggestions on this one.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the existing primer table and information dialog described in the issue, including annealed-versus-whole-primer values and PCR rows. Confirm the current display against the screenshots, then agree on warning thresholds and severity highlighting before changing the interface. Done means primer details are shown consistently and agreed warning states are visible.

Written by the indexing model from the issue text.

Assessment

Tech stack
javascript
Domain
frontend
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.