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Geneious: This is no spelling error!

Ashraf Amlani - Monday, January 31, 2011

To most people, the word "genius" brings to mind the image of Albert Einstein. But in the increasingly complicated world of biotechnology, the creation of simple, user friendly tools that process gigabytes of data within minutes and allow users to draw astounding conclusions is nothing short of genius. Since the only code most lab junkies are able to read involves the letters, A, T, G & C, analyzing large datasets of genetic code would be impossible without the help of our colleagues in computer science. Thankfully, many bioinformatic tools currently exist to allow scientists to analyze genomic data. SBN member, Mathew Lee, looks at one such program, Geneious, which is widely used in the genomics sector.

Are you frustrated with having to download your BLAST hit sequences individually?  Wanting to access multiple sequence analysis tools in one platform?  Geneious is just that gadget.  Since its creation in May 2006 by Biomatters Ltd, Geneious has undergone several updates to make it widely accessible and is compatible with the Windows, Mac OS X, Linux and Solaris operating systems. CheesecakeOn a completely irrelevant sidebar, one wonders whether the developers at Biomatters were simply craving dessert or if some hidden logic lies in naming Cheesecake, a software system that streamlines experimental protocols and data management for lab research.

Biomatters The free basic version offers sequence searching functions via accessing the various NCBI databases.  Sequence hits can be downloaded directly onto the user’s computer, and can be organized into folders.  In addition, Geneious offers basic sequence analysis tools to perform standard sequence alignments. Some free plug-ins for additional analysis tools are also available for download from the Geneious website.  Examples include MrBayes and PhyML, algorithms that allow for building phylogenetic trees from multiple sequence alignments.

While the basic version may sound attractive enough, there are even better advantages to using the Pro version.  For instance, additional analysis tools such as CLUSTALW and MUSCLE alignment algorithms, which enhance the accuracy of sequence alignments, are available in the Pro version.  A free 14-day trial of the Pro version is available, after which the user can either purchase a license or revert to using the free basic version.

Geneious Besides sequence importing and analysis capabilities, Geneious provides convenient, user-friendly image creation options.  For instance, columns of sequence alignments can be coloured according to different colouring schemes in order to facilitate analysis.  Furthermore, the sequence alignment can be saved as an image file in multiple formats such as JPG, PNG and PDF.

For progressing from sequence searching to analysis and image outputs in a single platform, Geneious is an excellent resource.  Analysis results and images can conveniently be saved locally on the user’s computer and be accessed later.  I definitely recommend trying out the program. 

Biomatters




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