SimiTriX-SimiTetra Files

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The relative similarity based on sequence alignment between different datasets such as whole genome provides the feasibility to get insights of biology, especially in the time of large-scale next generation sequencing. Several methods and tools to calculate and present the similarity are available, while many of them have its own shortcoming of algorithms. In addition, few of them provide user-friendly graphical user interface. Therefore, there is an urgent need for upgrading the functions and utility of previous tools. The availability of stable approaches to define the relative similarity relationship and visualize it conveniently would be beneficial for common biologists.

Significant efforts have been made to improve the utility. Here, we introduce the Similarity Triangle Extended and Similarity Tetrahedron (SimiTriX-SimiTetra) tool that provides researchers a quick and easy way to analysis and visualize relative similarity. In detail, we combined the methods of Blast Raw Score and Blast Score Ratio mentioned in SimiTri and BSR approach to classify the elements in reference dataset using a measure of similarity relationship relative to three other different datasets. Meanwhile, a new algorithm based on the transformation of blast score to coordinate in triangle was proposed to solve the situation that comparing elements in reference dataset with four other associated datasets by restricting elements within a tetrahedron. In order to improve the utility of above approaches, both user-friendly stand-alone version and web server version were mainly implemented in Java and WebGL (Web Graphics Library) technology. Furthermore, we applied it to take insight into the inter-genomic relationship between cotton (Gossypium raimondii) with four other plant species by whole genome blast.

This project is the stand-alone version of the SimiTriX-SimiTetra application. It was built on the Eclipse RCP framework. More information can be got in the "help" section of this software.

The BioERCP(SimiTriX-SimiTetra) is based on the origin SimiTri algorithm and Blast Score Ratio(BSR) method. If you want to see more about the SimiTri and BSR method, you can read the following papers:

Two main references:
1. Parkinson J, Blaxter M. SimiTri--visualizing similarity relationships for groups of sequences. Bioinformatics. 2003 Feb 12;19(3):390-5
2. Rasko DA, Myers GS, Ravel J. Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics. 2005, 6:2

If you have any question about this project, please contact me by email
gaowenhui2012@gmail.com

update time:
#2013-8-9
Upload the first verion of BioERCP to the sourceforge.net.