Genomic Spring-Synteny Visualization with IMAS

Author

Shaw, Chris D.

Author_Institution

Sch. of Interactive Arts & Technol., Simon Fraser Univ., Surrey, BC

fYear

2008

fDate

9-11 July 2008

Firstpage

3

Lastpage

8

Abstract

This paper presents a synteny visualization and analysis tool developed in connection with IMAS - the Interactive Multigenomic Analysis System. This visual analysis tool enables biologists to analyze the relationships among genomes of closely related organisms in terms of the locations of genes and clusters of genes. A biologist starts IMAS with the DNA sequence, uses BLAST to find similar genes in related sequences, and uses these similarity linkages to create an enhanced node-link diagram of syntenic sequences. We refer to this as Spring Synteny visualization, which is aimed at helping a biologist discover similar gene ordering relationships across species. The paper describes the techniques that are used to support synteny visualization, in terms of computation, visual design, and interaction design.

Keywords

DNA; biology computing; data visualisation; genetics; molecular biophysics; BLAST; DNA sequence; IMAS; Interactive Multigenomic Analysis System; closely related organisms; gene cluster locations; gene locations; gene ordering relationships; genome relationship analysis; genomic spring-synteny visualization; interaction design; related gene sequences; similar gene search; similarity linkages; syntenic sequence enhanced node-link diagram; synteny analysis tool; visual analysis tool; visual design; Bioinformatics; Biological information theory; DNA; Databases; Displays; Genomics; Information analysis; Organisms; Sequences; Visualization; Bioinformatics; Sequence Analysis; Visual Analytics;

fLanguage

English

Publisher

ieee

Conference_Titel

BioMedical Visualization, 2008. MEDIVIS '08. Fifth International Conference

Conference_Location

London

Print_ISBN

978-0-7695-3284-4

Type

conf

DOI

10.1109/MediVis.2008.17

Filename

4618606