ApE 1.17

An easy to use plasmid editor for your Mac
ApE - The Enzymes menu helps you list, select and view the graphic map for enzymes.
  7 Screenshots
ApE is an easy to use plasmid analysis and editor software for your Mac.

Main features:

  • Runs on Mac OS X (10.3, 10.4 and 10.5), Windows (tested on 98, XP, NT), and Linux/Unix
  • Highlights restriction sites in the editing window
  • Accurately reflects Dam/Dcm blocking of enzyme sites
  • Highlights text using pre-defined and custom feature libraries
  • 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 embl 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 (for snip-SNP detection or diagnostic digests)
  • Has user defined enzyme grouping to distiguish eg. enzymes currently in stock.
  • Allows users to define new enzymes by name and recognition site
  • Imports DNA Strider format files (simple enzyme, site lists) 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
  • 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
  • Translates sequences with optional DNA alignment
  • Finds potential primers matching user criteria (length, Tm, %GC, self/other complementarity)
  • Aligns two DNA sequences (or any combination of sequence and ABI trace), with the alignment hyperlinked to the original sequence
  • Finds translationally silent restriction sites
  • Draws graphic ORF maps

last updated on:
January 10th, 2011, 6:50 GMT
file size:
4 MB
price:
FREE!
license type:
Donationware 
developed by:
M. Wayne Davis
operating system(s):
Mac OS X
binary format:
Universal Binary
category:
Home \ Math/Scientific
ApE
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7 Screenshots
ApE - Using the Tools menu will help you find primers, align sequences and download sequences from NCBI.ApEApEApEApEApE

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