ApE- A Plasmid Editor

What you can do:
Edit, annotate and draw plasmid sequences.
  • This free software tool allows a user to perform various tasks on plasmid sequence.
  • Features including:
  • Highlights restriction sites in the editing window
  • Accurately reflects Dam/Dcm blocking of enzyme sites
  • Highlights text using pre-defined and custom feature libraries
  • Highlights text using user defined features
  • Shows translation, Tm, %GC, ORF of selected DNA in real-time
  • Reads DNA Strider, Fasta, Genbank and EMBL files
  • Saves files as DNA Strider-compatible or Genbank file format
  • Highlights and draws graphic maps using feature annotations from Genbank and EBML files
  • Directly BLASTs selected sequence at NCBI or wormbase
  • Text map shows DNA sequence, translation, and features as text-based graphics
  • Creates graphic restriction maps- linear or circular with features indicated
  • Connects graphic and text features with hyperlink double click
  • Saves graphics as encapsulated postscript or scalable vector graphics
  • Copy and save graphics as Windows metafiles (MS Windows only)
  • Virtual restriction digest
  • Draws pre-defined and user-defined DNA ladders
  • Connects bands to text by double-click
  • Reads ABI sequencing trace files
  • Sequences in ABI traces can be aligned directly to a reference sequence, with the alignment hyperlinked back to te trace.
  • Selects sites matching multiple criteria (union/intersection- cut frequency, site type) in all open windows
  • Selects sites that cut more often in one sequence than another
  • Has user defined enzyme grouping to distinguish eg. enzymes currently in stock.
  • Allows users to define new enzymes by name and recognition site
  • Imports DNA Strider format files available from REBASE
  • Most analysis windows are hyperlinked to their corresponding sequences, including:
  • Graphic Maps
  • Text maps
  • Virtual Digests
  • Alignments (including ABI sequences)
  • Silent Sites
  • Translation
  • Primer Find
  • sequence manipulation tool
  • sequence editor
  • plasmid design tool
  • vector design tool
Literature & Tutorials:
This record last updated: 01-25-2006

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