GENtle/DNA map

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 on	Mouse button	Function
Background	left	Mark sequence
	left (double click)	Open Sequence editor
	middle	Show marked DNA in sequence; show current position in sequence if nothing is marked
Feature	left	Move feature display
	left (double click)	Edit feature (see Sequence editor)
	middle	Mark DNA that matches feature
	middle (shift pressed)	Extend currently marked area to include the DNA of the feature
Restriction site	left	Move site display
	left (double click)	Edit enzyme list (see Sequence editor)
	middle	Open Restriction Assistant
Open reading frame	left	Mark ORF sequence
	left (double click)	Mark and show ORF sequence
All	right	Context 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 sequence	Opens the Sequence editor
Transform sequence	Make sequence inverted and/or complementary
Limit enzymes	Limits enzymes to those that cut no more than n times
PCR/PCR	Starts the PCR modul
PCR/Forward	Starts the PCR modul and generates a 5'->3'-primer
PCR/Backward	Starts the PCR modul and generates a 5'->3'-primer
PCR/Both	Starts the PCR modul and generates both primers
PCR/Mutation	Starts the PCR modul and generates overlapping mutagenesis primers
Selection/Cut	Removes the selected part of the sequence and puts it into the clipboard
Selection/Copy	Copys the selected part of the sequence into the clipboard
Selection/Copy to new sequence	Generate a new DNA sequence entry based on the selection
Selection/Show enzymes that cut here	Opens a variant of the Silent Mutagenesis dialog for the selected part of the sequence
Selection/Selection as new feature	Generates a new feature for the selected part of the sequence
Selection/Extract amino acids	Extracts the amino acid sequence of the selected part of the DNA sequence
Selection/BLAST amino acids	Runs a BLAST search for the amino acid sequence of the selected part of the DNA sequence
Selection/BLAST DNA	Runs a BLAST search for the selected part of the DNA sequence
Sequence map/Save as image	Saves the DNA map as an image file
Sequence map/Copy image to clipboard	Copies the DNA map as a bitmap or WMF (see Options) to the clipboard
Sequence map/Print map	Prints the DNA map
Show/hide ORFs	Toggles the open reading frame display
Edit ORFs	Adjusts the open reading frame display

Restriction sites

Edit restriction enzyme	Add/remove/manage restriction enzyme via the Sequence editor
Show/hide enzyme	Toggle visibility for the enzyme (this will affect all restriction sites for that enzyme in this sequence)
Remove enzyme	Remove 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 site	Marks the recognition sequence of that enzyme at that restriction site
Mark and show restriction site	Marks the recognition sequence of that enzyme at that restriction site and shows it in the sequence
Online enzyme information	Opens the ReBase page for that enzyme
Add to cocktail	This adds the enzyme to the restriction cocktail (see Restriction Assistant)
Add to cocktail	This adds the enzyme to the restriction cocktail (see Restriction Assistant) and starts the restriction

Features

Edit feature	Edit the feature properties (see GENtle/Sequence editor)
Hide feature	Hide the feature from display
Delete feature	Delete the feature
DNA Sequence/Mark feature sequence	Mark the DNA sequence that matches the feature
DNA Sequence/Mark and show feature sequence	Mark the DNA sequence that matches the feature and shows it in the sequence
DNA Sequence/Copy (coding) DNA sequence	Copies the DNA sequence that matches the feature to the clipboard
DNA Sequence/This feature as new sequence	Generates a new DNA sequence based on the feature
DNA Sequence/BLAST DNA	Runs a BLAST search for the DNA of the feature
Amino acid sequence/Copy amino acid sequence	Copies the amino acid sequence of the feature to the clipboard
Amino acid sequence/As new entry	Generates a new protein entry based on the amino acid sequence of the feature
Amino acid sequence/Blast amino acids	Runs a BLAST search for the amino acid sequence of the feature

Open reading frames

As new feature	Generate a new feature from the ORF, with the appropriate reading frame and direction
DNA sequence/Copy DNA sequence	Copies the DNA sequence of the ORF to the clipboard
DNA sequence/As new DNA	Generates a new DNA sequence entry based on the DNA sequence of the ORF
DNA sequence/BLAST DNA	Runs a BLAST search for the DNA sequence of the ORF
Amino acid sequence/Copy amino acid sequence	Copies the amino acid sequence of the ORF to the clipboard
Amino acid sequence/As new AA	Generates a new protein entry based on the amino acid sequence of the ORF
Amino acid sequence/BLAST amino acids	Runs a BLAST search for the amino acid sequence of the ORF