ApE - A Plasmid Editor (software review): Difference between revisions

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[[Image:ApE sequence view w markup.png|right|300px|thumb|ApE sequence file in text view with feature highlights]]
[[Image:ApE sequence view w markup.png|right|300px|thumb|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.
'''ApE''' is a proprietary 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 ==
== Features ==
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The author is very responsive and integrated a BankIt export option, I suggested, within a few days. --[[User:Jakob Suckale|JS]] 05:50, 30 June 2010 (EDT)
The author is very responsive and integrated a BankIt export option, I suggested, within a few days. --[[User:Jakob Suckale|JS]] 05:50, 30 June 2010 (EDT)
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There is a serious bug affecting the alignment function in recent versions of ApE, including the current release (2.0.45).  In some cases where the sequences differ by a single base-pair indel, the alignment output by ApE is incorrect and the mismatching residues are not highlighted in red as expected.  This can make it very easy to miss small deletions when checking your sequencing data against the expected sequence. --[[User:Damian Ekiert|Damian Ekiert]] 12:19, 22 February 2013 (EST)
<b>There is a serious bug affecting the alignment function in recent versions of ApE (I have encountered it in 2.0.39 - 2.0.45 at least, may affect all 2.0.X versions?) released over the last ~12 months, including the current release (2.0.45).</b> In some cases where the sequences differ by a single base-pair indel, the alignment output by ApE is incorrect and the mismatching residues are not highlighted in red as expected.  This can make it very easy to miss small deletions when checking your sequencing data against the expected sequence. This should be corrected in the yet-to-be-released version 2.0.46.  See bug report [http://ape-a-plasmid-editor.wikispaces.com/Potential+Bugs here] ("Misalignment of sequences with indels (sometimes)"). Use with caution! --[[User:Damian Ekiert|Damian Ekiert]] 12:19, 22 February 2013 (EST).  '''The [http://biologylabs.utah.edu/jorgensen/wayned/ape/ current version], v2.0.46, doesn't have this issue, says [http://ape-a-plasmid-editor.wikispaces.com/Potential+Bugs bug report]''' -- [[User:Janet B. Matsen|JM 9/2013]]


== Links to the ApE homepage ==
== Links to the ApE homepage ==

Latest revision as of 08:05, 31 October 2013

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 proprietary 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)

There is a serious bug affecting the alignment function in recent versions of ApE (I have encountered it in 2.0.39 - 2.0.45 at least, may affect all 2.0.X versions?) released over the last ~12 months, including the current release (2.0.45). In some cases where the sequences differ by a single base-pair indel, the alignment output by ApE is incorrect and the mismatching residues are not highlighted in red as expected. This can make it very easy to miss small deletions when checking your sequencing data against the expected sequence. This should be corrected in the yet-to-be-released version 2.0.46. See bug report here ("Misalignment of sequences with indels (sometimes)"). Use with caution! --Damian Ekiert 12:19, 22 February 2013 (EST). The current version, v2.0.46, doesn't have this issue, says bug report -- JM 9/2013

Links to the ApE homepage

See also

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