ApE (A Plasmid Editor) is a small, easy to use plasmid editor. ApE was developed to be a small, easy to use plasmid editor.
ApE Features:
1. Runs in Windows (tested on 98, XP, NT), OS X(10.3, 10.4 and 10.5), and Linux/Unix
2. Highlights restriction sites in the editing window
3. Accurately reflects Dam/Dcm blocking of enzyme sites
4. Highlights text using pre-defined and custom feature libraries
5. Shows translation, Tm, %GC, ORF of selected DNA in real-time
6. Reads DNA Strider, Fasta, Genbank and EMBL files
7. Saves files as DNA Strider-compatible or Genbank file format
8. Highlights and draws graphic maps using feature annotations from genbank and embl files
9. Directly BLASTs selected sequence at NCBI or wormbase
10. Text map shows DNA sequence, translation, and features as text-based graphics
11. Creates graphic restriction maps- linear or circular with features indicated
12. Connects graphic and text features with hyperlink double click
13. Saves graphics as encapsulated postscript or scalable vector graphics
14. Copy and save graphics as Windows metafiles (MS Windows only)
15. Virtual restriction digest
16. Draws pre-defined and user-defined DNA ladders
17. Connects bands to text by double-click
18. Reads ABI sequencing trace files
19. Sequences in ABI traces can be aligned directly to a reference sequence, with the alignment hyperlinked back to te trace.
20. Selects sites matching multiple criteria (union/intersection- cut frequency, site type) in all open windows
21. Selects sites that cut more often in one sequence than another (for snip-SNP detection or diagnostic digests)
22. Has user defined enzyme grouping to distiguish eg. enzymes currently in stock.
23. Allows users to define new enzymes by name and recognition site
24. Imports DNA Strider format files (simple enzyme, site lists) available from REBASE

Other Features:
1. Most analysis windows are hyperlinked to their corresponding sequences, includes:
* Graphic Maps
* Text maps
* Virtual Digests
* Alignments (including ABI sequences)
* Silent Sites
* Translation
* Primer Find

2. Uses custom feature definition libraries, which allow:
* Quick annotation of sequence
* Quick searching and highlighting of all available primers that you (or others) have that hybridize to a sequence
* Sequence to be annotated and visualized in multiple ways quickly and efficiently
* Graphic maps that show primer binding sites and all interesting sequence features

3. Translates sequences with optional DNA alignment
4. Finds potential primers matching user criteria (length, Tm, %GC, self/other complementarity)
5. Aligns two DNA sequences (or any combination of sequence and ABI trace), with the alignment hyperlinked to the original sequence
6. Finds translationally silent restriction sites
7. Draws graphic ORF maps

The license of this software is Freeware, you can free download and free use this calculator software.