Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

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SRD: A Universal Software Tool for DNA/Protein Sequence Relationship Visualization Based on Undirected Graphs

Author(s): Ning Zhang, Shan Gao, Guangyou Duan, Yuanming Feng, Jishou Ruan, Tao Zhang.

Graphical Abstract:


Abstract:

In an effort to accelerate translational bioinformatics research, this study presents a universal software tool, named as Sequence Relation Drawing program (SRD). It can be used to dynamically visualize the relationship between molecular sequences and their categories based on undirected graphs in similarity analysis of gene and protein sequences. SRD consists of two components: a Window-based application and a computerized database. Researchers can import their datasets into the database, which will make the software run faster and occupy less memory. Pre-computed sequence relations and other user-defined information can also be imported into the system, and then be visualized in several interactive perspectives. Sequences could be partitioned into several categories, and several windows are provided and linked for the visualization involving intro-category, extra-category and category-category relationships, respectively. An example is also provided, which is HIV Pestiferous Map Analysis. Given the sequences of the envelope glycoprotein gene and their similarities, SRD could help to investigate traits of the spread of the AIDS disease, which may help biologists or clinicians to control the AIDS disease transmission in molecular epidemiology study. The SRD software can be download from http://www.nkbiox.com/srd/index.htm.

Keywords: Categories map, sequence similarity, translational bioinformatics, undirected graph, visualization.

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Article Details

VOLUME: 10
ISSUE: 1
Year: 2015
Page: [69 - 78]
Pages: 10
DOI: 10.2174/157489361001150309141803