GENtle/DNA map

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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

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[edit]

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[edit]

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[edit]

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]

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]

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]

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[edit]

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