BioWord: A sequence manipulation suite for Microsoft Word

BMC Bioinformatics

Software

Daniel Muñoz-Fernández¹  Laura J Anzaldi²  Ivan Erill³ 

[1] Departament de Ciències de la Computació, Universitat Autònoma de Barcelona, Campus UAB s/n, 08193, Bellaterra, Barcelona, Spain;Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, 21250, Baltimore, MD, USA;Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, 21250, Baltimore, MD, USA;Departament de Ciències de la Computació, Universitat Autònoma de Barcelona, Campus UAB s/n, 08193, Bellaterra, Barcelona, Spain;

关键词: Motif Discovery;    Sequence Logo;    Greedy Search;    Sequence Object;    Sequence Manipulation;   

DOI  :  10.1186/1471-2105-13-124

 received in 2012-01-03, accepted in 2012-05-10,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools.ResultsBioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs.ConclusionsBioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms.

【 授权许可】

Unknown   
© Anzaldi et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.