ApE - A Plasmid Editor (software review)

ApE sequence file viewed in linear schematic representation with sequence feature markup

ApE sequence filed viewed in circular schematic representation

ApE sequence file in text view with feature highlights

ApE is a very useful sequence editor using a modified GenBank format to save sequences. 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.

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

Comments

The author is very responsive and integrated a BankIt export option, I suggested, within a few days. --JS 05:50, 30 June 2010 (EDT)

Links to the ApE homepage

• ApE plasmid editor homepage & downloads
• ApE wiki for question, answers, feature requests, bug reports, etc.
• download latest preview versions (alphas)

See also

• ApE review at softpedia
• An OWW tutorial using ApE
• Wikiomics:Bioinfo tutorial#DNA sequence processing
• Biosoftware for Mac
• Sequence analysis