ApE - A Plasmid Editor (software review)

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Revision as of 05:36, 30 June 2010 by Jakob Suckale (Talk | contribs)
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ApE is a very useful sequence editor which saves sequences in a modified GenBank format. The software can be used for assembly of sequencing traces, virtual digests, sequence annotation, and schematic sequence representation. It was created and is maintained by Wayne Davis from the University of Utah. The current stable version, as of June 2010, is 1.17 and the software runs on Windows, Mac, and Unix. The software is free but donations are encouraged.

Contents

Features

OS, data format

  • runs on Windows, OS X, and Linux/Unix
  • imports DNA Strider, Fasta, Genbank, EMBL and ABI sequence traces
  • saves data in a modified Genbank file format (DNA Strider-compatible)
  • exports BankIt feature table for sequence submission to NCBI GenBank
  • export graphic files of sequence diagrams

Sequence markup and tools

  • pre-existing expandable feature tables which can be used for automatic annotation
  • sequence search, e.g. for primers, probes, or restriction sites
  • restriction sites and region markup in sequence and in a simple cartoon
  • shows translation, Tm, %GC, ORF of selected DNA
  • BLAST selected sequence at NCBI or wormbase
  • virtual digest including gel diagram

Links to the ApE homepage

See also

Personal tools