GENtle/Sequencing Primers

From Wikibooks, open books for an open world
< GENtle
Jump to: navigation, search
GENtle splash screen.png The GENtle manual

About - FAQ - Setup - DNA - Protein - PCR and Primer Design - Sequencing - Alignments - Calculators - Virtual Gel - Image Viewer - Tools and Dialogs - Web interface - Graphs and plots - DNA map - Sequence map - Dot plot - Restriction Identifier

Sequencing primers dialog

The sequencing primers dialog can add possible sequencing primers as features to a DNA sequence. What primers to add can be specified:

  • The minimum alignment (3') of a primer to the sequence. This means exact annealing!
  • The database to search for primers. All primers from that database will be considered.
  • Alternatively, use all primers that are part of a project in that database. That way, a range of primers across databases can be specified in a project and be considered as sequencing primers here.
  • Primers that run in 5'→3' or 3'→5' direction.

You can also have the dialog remove old sequencing primers from the sequence. This can also be done manually through Edit/Remove sequencing primers in the DNA module. Note: Sequencing primers, if not removed, will be saved as features together with the sequence; they can still be removed lated, though.

Sequencing primers will display as yellow features, where the shade of yellow depends on their direction. The actual sequencing primer feature is only as long as the 3' annealing of the primer, so the primer might actually be longer than the feature towards the 5' end. For details, see the feature description, which contains the original primer sequence, among other data.