GENtle/DNA map

__NOTOC__ thumb|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 buttonFunctionBackgroundleftMark sequenceleft (double click)Open ../Sequence editor/middleShow marked DNA in sequence; show current position in sequence if nothing is markedFeatureleftMove feature displayleft (double click)Edit feature (see ../Sequence editor/)middleMark DNA that matches featuremiddle (shift pressed)Extend currently marked area to include the DNA of the featureRestriction siteleftMove site displayleft (double click)Edit enzyme list (see ../Sequence editor/)middleOpen ../Restriction Assistant/Open reading frameleftMark ORF sequenceleft (double click)Mark and show ORF sequenceAllrightContext 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 complementaryLimit enzymesLimits enzymes to those that cut no more than n timesPCR/PCRStarts the PCR modulPCR/ForwardStarts the PCR modul and generates a 5'->3'-primerPCR/BackwardStarts the PCR modul and generates a 5'->3'-primerPCR/BothStarts the PCR modul and generates both primersPCR/MutationStarts the PCR modul and generates overlapping mutagenesis primersSelection/CutRemoves the selected part of the sequence and puts it into the clipboardSelection/CopyCopys the selected part of the sequence into the clipboardSelection/Copy to new sequenceGenerate a new DNA sequence entry based on the selectionSelection/Show enzymes that cut hereOpens a variant of the ../Silent Mutagenesis/ dialog for the selected part of the sequenceSelection/Selection as new featureGenerates a new feature for the selected part of the sequenceSelection/Extract amino acidsExtracts the amino acid sequence of the selected part of the DNA sequenceSelection/BLAST amino acidsRuns a BLAST search for the amino acid sequence of the selected part of the DNA sequenceSelection/BLAST DNARuns a BLAST search for the selected part of the DNA sequenceSequence map/Save as imageSaves the DNA map as an image fileSequence map/Copy image to clipboardCopies the DNA map as a bitmap or WMF (see ../Options/) to the clipboardSequence map/Print mapPrints the DNA mapShow/hide ORFsToggles the open reading frame displayEdit 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 siteMark and show restriction siteMarks the recognition sequence of that enzyme at that restriction site and shows it in the sequenceOnline enzyme informationOpens the ReBase page for that enzymeAdd 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 ../Sequence editor)Hide featureHide the feature from displayDelete featureDelete the featureDNA Sequence/Mark feature sequenceMark the DNA sequence that matches the featureDNA Sequence/Mark and show feature sequenceMark the DNA sequence that matches the feature and shows it in the sequenceDNA Sequence/Copy (coding) DNA sequenceCopies the DNA sequence that matches the feature to the clipboardDNA Sequence/This feature as new sequenceGenerates a new DNA sequence based on the featureDNA Sequence/BLAST DNARuns a BLAST search for the DNA of the featureAmino acid sequence/Copy amino acid sequenceCopies the amino acid sequence of the feature to the clipboardAmino acid sequence/As new entryGenerates a new protein entry based on the amino acid sequence of the featureAmino 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 directionDNA sequence/Copy DNA sequenceCopies the DNA sequence of the ORF to the clipboardDNA sequence/As new DNAGenerates a new DNA sequence entry based on the DNA sequence of the ORFDNA sequence/BLAST DNARuns a BLAST search for the DNA sequence of the ORFAmino acid sequence/Copy amino acid sequenceCopies the amino acid sequence of the ORF to the clipboardAmino acid sequence/As new AAGenerates a new protein entry based on the amino acid sequence of the ORFAmino acid sequence/BLAST amino acidsRuns a BLAST search for the amino acid sequence of the ORF