Nonetheless, the use of JavaScript results also in some limitations, like the inability to access files on the client computer, which forces the user to rely on copying and pasting data in text format. Web-based sequence editing toolkits like SMS have enjoyed wide acceptance because they provide a simple interface for many routine sequence manipulation tasks and because, running on JavaScript, they are essentially platform independent. To perform these routine manipulations, this substantial segment of users has resorted to proprietary desktop software, like DNAStar or the GCG Wisconsin Package, ingenious bookmarking of specific web servers, or to services that integrate several tools for sequence manipulation, like the Molecular Toolkit or the Sequence Manipulation Suite (SMS). Still, a wide range of practicing biologists must routinely perform relatively simple manipulation, editing and processing of DNA and protein sequences on a daily basis. BLAST and Entrez search) and lack the necessary training in bioinformatics to navigate easily through interconnected repositories of data and services. The sheer scope and power of data and service integration portals and browser add-ons is also one of the main obstacles to their wide acceptance, since many users rarely need to use more than one or two services (e.g. Many of these approaches have relied on the creation of web-based service portals that seek to integrate and simplify data collection analysis with a wide variety of available tools, while other efforts have focused on service and data integration through the use of browser-enabled interoperability between services, data providers and even desktop applications. There have been several attempts to reconcile this vast and expanding array of services with data and service integration. At the same time, the number of tools and servers for performing analyses on biological sequences and related data has exploded, creating a need for resource integration. In a relatively short time, editing and processing of DNA and protein sequences have left the realm of molecular biology to become a routine practice for biologists working in myriad different fields. 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.
ARE SEQUENCE LOGOS BETTER THAN CONSENSUS SEQUENCES SOFTWARE
ConclusionsīioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. 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. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. After installation, BioWord will open as a tab in the Office ribbon. ResultsīioWord is distributed as a single macro-enabled template that self-installs with a single click. 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. 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. The 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.
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