ApE- A Plasmid Editor
What you can do:
Edit, annotate and draw plasmid sequences.
Highlights:
- 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
Keywords:
- sequence manipulation tool
- sequence editor
- plasmid design tool
- vector design tool
Literature & Tutorials:
This record last updated: 01-25-2006