title: Identification of simple sequence repeat biomarkers through cross-species comparison in a tag cloud representation.
abstract: Simple sequence repeats (SSRs) are not only applied as genetic markers in evolutionary studies but they also play an important role in gene regulatory activities. Efficient identification of conserved and exclusive SSRs through cross-species comparison is helpful for understanding the evolutionary mechanisms and associations between specific gene groups and SSR motifs. In this paper, we developed an online cross-species comparative system and integrated it with a tag cloud visualization technique for identifying potential SSR biomarkers within fourteen frequently used model species. Ultraconserved or exclusive SSRs among cross-species orthologous genes could be effectively retrieved and displayed through a friendly interface design. Four different types of testing cases were applied to demonstrate and verify the retrieved SSR biomarker candidates. Through statistical analysis and enhanced tag cloud representation on defined functional related genes and cross-species clusters, the proposed system can correctly represent the patterns, loci, colors, and sizes of identified SSRs in accordance with gene functions, pattern qualities, and conserved characteristics among species.
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan.
authors.forename: Jhen-Li
authors.identifier: 0000-0002-6560-074X
authors.initials: JL
authors.lastname: Huang
authors.affiliation: Graduate Institute of Basic Medical Science, China Medical University, Taichung City 40402, Taiwan ; Department of Computer Science and Information Engineering, Asia University, Taichung City 41354, Taiwan.
authors.forename: Hao-Teng
authors.identifier: 0000-0001-8756-5220
authors.initials: HT
authors.lastname: Chang
authors.affiliation: Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan.
authors.forename: Ronshan
authors.identifier: 0000-0002-2483-1218
authors.initials: R
authors.lastname: Cheng
authors.affiliation: Department of Computer Science and Information Engineering, Tamkang University, New Taipei City 25137, Taiwan.
authors.forename: Hui-Huang
authors.identifier: 0000-0003-1243-7405
authors.initials: HH
authors.lastname: Hsu
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan.
authors.forename: Tun-Wen
authors.identifier: 0000-0002-2869-4169
authors.initials: TW
authors.lastname: Pai
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D005819:Genetic Markers / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D008957:Models, Genetic; D013045:Species Specificity
chemical_list: D005819:Genetic Markers; D004247:DNA