< GENtle
The DNA map.

The DNA map is shown for DNA sequences (though a variant is also used in protein module for the schematics display). It shows the linear or circular (e.g., plasmid) DNA sequence as a map.

Display

Displayed are

  • features (including optional sequencing primers)
  • restriction sites
  • sticky ends (if any)
  • open reading frames (optional)
  • sequence name and length (optional, see Options)
  • methylation (optional, see Options)
  • GC contents (optional, see Options)

Mouse actions

Action onMouse buttonFunction
Background leftMark sequence
left (double click)Open Sequence editor
middleShow marked DNA in sequence; show current position in sequence if nothing is marked
Feature leftMove feature display
left (double click)Edit feature (see Sequence editor)
middleMark DNA that matches feature
middle (shift pressed)Extend currently marked area to include the DNA of the feature
Restriction site leftMove site display
left (double click)Edit enzyme list (see Sequence editor)
middleOpen Restriction Assistant
Open reading frame leftMark ORF sequence
left (double click)Mark and show ORF sequence
AllrightContext menu

Context menu

The context menu opens on a click with the right mouse button when somewhere inside the DNA map. The contents of the menu depends on what object in the map you clicked on. Also, depending on the properties of the object, some functions might not be available, for example, amino acids of a feature with no reading frame.

Background

Edit sequenceOpens the Sequence editor
Transform sequenceMake sequence inverted and/or complementary
Limit enzymesLimits enzymes to those that cut no more than n times
PCR/PCRStarts the PCR modul
PCR/ForwardStarts the PCR modul and generates a 5'->3'-primer
PCR/BackwardStarts the PCR modul and generates a 5'->3'-primer
PCR/BothStarts the PCR modul and generates both primers
PCR/MutationStarts the PCR modul and generates overlapping mutagenesis primers
Selection/CutRemoves the selected part of the sequence and puts it into the clipboard
Selection/CopyCopys the selected part of the sequence into the clipboard
Selection/Copy to new sequenceGenerate a new DNA sequence entry based on the selection
Selection/Show enzymes that cut hereOpens a variant of the Silent Mutagenesis dialog for the selected part of the sequence
Selection/Selection as new featureGenerates a new feature for the selected part of the sequence
Selection/Extract amino acidsExtracts the amino acid sequence of the selected part of the DNA sequence
Selection/BLAST amino acidsRuns a BLAST search for the amino acid sequence of the selected part of the DNA sequence
Selection/BLAST DNARuns a BLAST search for the selected part of the DNA sequence
Sequence map/Save as imageSaves the DNA map as an image file
Sequence map/Copy image to clipboardCopies the DNA map as a bitmap or WMF (see Options) to the clipboard
Sequence map/Print mapPrints the DNA map
Show/hide ORFsToggles the open reading frame display
Edit ORFsAdjusts the open reading frame display

Restriction sites

Edit restriction enzymeAdd/remove/manage restriction enzyme via the Sequence editor
Show/hide enzymeToggle visibility for the enzyme (this will affect all restriction sites for that enzyme in this sequence)
Remove enzymeRemove the enzyme from the current selection (this will affect all restriction sites for that enzyme in this sequence).
This will not work for automatically added enzymes (see Options)
Mark restriction siteMarks the recognition sequence of that enzyme at that restriction site
Mark and show restriction siteMarks the recognition sequence of that enzyme at that restriction site and shows it in the sequence
Online enzyme informationOpens the ReBase page for that enzyme
Add to cocktailThis adds the enzyme to the restriction cocktail (see Restriction Assistant)
Add to cocktailThis adds the enzyme to the restriction cocktail (see Restriction Assistant) and starts the restriction

Features

Edit featureEdit the feature properties (see GENtle/Sequence_editor)
Hide featureHide the feature from display
Delete featureDelete the feature
DNA Sequence/Mark feature sequenceMark the DNA sequence that matches the feature
DNA Sequence/Mark and show feature sequenceMark the DNA sequence that matches the feature and shows it in the sequence
DNA Sequence/Copy (coding) DNA sequenceCopies the DNA sequence that matches the feature to the clipboard
DNA Sequence/This feature as new sequenceGenerates a new DNA sequence based on the feature
DNA Sequence/BLAST DNARuns a BLAST search for the DNA of the feature
Amino acid sequence/Copy amino acid sequenceCopies the amino acid sequence of the feature to the clipboard
Amino acid sequence/As new entryGenerates a new protein entry based on the amino acid sequence of the feature
Amino acid sequence/Blast amino acidsRuns a BLAST search for the amino acid sequence of the feature

Open reading frames

As new featureGenerate a new feature from the ORF, with the appropriate reading frame and direction
DNA sequence/Copy DNA sequenceCopies the DNA sequence of the ORF to the clipboard
DNA sequence/As new DNAGenerates a new DNA sequence entry based on the DNA sequence of the ORF
DNA sequence/BLAST DNARuns a BLAST search for the DNA sequence of the ORF
Amino acid sequence/Copy amino acid sequenceCopies the amino acid sequence of the ORF to the clipboard
Amino acid sequence/As new AAGenerates a new protein entry based on the amino acid sequence of the ORF
Amino acid sequence/BLAST amino acidsRuns a BLAST search for the amino acid sequence of the ORF
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