Title:SRD: A Universal Software Tool for DNA/Protein Sequence Relationship Visualization Based on Undirected Graphs
Volume: 10
Issue: 1
Author(s): Ning Zhang, Shan Gao, Guangyou Duan, Yuanming Feng, Jishou Ruan and Tao Zhang
Affiliation:
Keywords:
Categories map, sequence similarity, translational bioinformatics, undirected graph, visualization.
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.
