DNA annotation or genome annotation is the process of (a) identifying the locations/segments of genes, coding regions and other specific locations that are of imporatance in a DNA sequence or genome and (b) associating relevant information with those locations/segments (e.g. determining what the identified genes do). Once a genome is sequenced, it needs to be annotated in order to make sense of it.

Target audience/users: Molecular biologists and those who work in the field of Bioinformatics and also those enthusiastic software professionals who wish to work in the informatics part of the much larger universe of biological research.

The goal and the focus in building and publishing the first version of this tool was to demonstrate the possibilities and power of such tools. The current release has useful features, which are listed below - please download and use the tool. The current version has certain obvious limitations. For the future versions many more enhancements have been planned.

DNA & RNA Sequence Annotation Studio is a very useful sequence annotation visualization and modification tool and can be used to perform the following actions:

1. Load DNA or RNA sequences in GenBank format and visualize the complete sequence with zoom in / zoom out facility.
The current version only handles GenBank format (for details on GenBank format, please refer to GenBank Format), although it can be easily enhanced to support other formats. The current version only handles one sequence per file. Therefore, if an input file contains multiple sequences, only the first sequence will be loaded; in order to view/modify remaining sequence(s) in the input file, separate input files need to be created.

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2. View all the annotations associated with the loaded sequence. Details (Annotation Qualifiers) about a particular annotation can be viewed either by hovering the mouse over the annotation or by selecting the edit button.

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3. Create new annotations and edit or delete existing ones. New annotations can be added either selecting (by clicking and dragging the mouse) or not selecting a sub-sequence by mouse. While creating/editing annotations, applicable qualifiers (for the selected annotation type, also called GenBank feature key) can be added, modified or deleted. Three data types for the qualifiers are supported: string, list of strings and boolean.

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add-1.png

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edit_delete.png

edit-1.png

edit-2.png

delete-1.png

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and finally,

4. Save modified sequence in GenBank format.

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The following features of Microsoft Biology Foundation 2.0 Beta have been used to build the tool

  • GenBank parser
  • GenBank Formatter
  • Sequence and associated classes/data structures, FeatureItem (to represent annotations)
  • Location and LocationBuilder
  • StandardFeatureKeys, StandardQualifierNames and StandardFeatureMap



The tool has been built using

  • Windows Presentation Foundation 4.0
  • Visual Studio 2010 IDE
  • Microsoft Biology Foundation 2.0 Beta 1



System requirements for use

  • .NET framework 4.0, which can be downloaded from here.

Last edited Aug 7, 2011 at 8:10 AM by kajaldas007, version 36