An algorithm for detecting isochore boundaries using a new technique of GCDT

Author

Wang, Anhui ; Chang, Guiran ; Deng, Xuemei ; Deng, Xuegong

Author_Institution

Sch. of Inf. Sci. & Eng., Northeastern Univ., Shenyang, China

Volume

2

fYear

2009

fDate

8-9 Aug. 2009

Firstpage

262

Lastpage

265

Abstract

A novel visualization method named GCDT has been proposed to calculate and display the GC contents of genomes of different organisms. Based on the GCDT method, a new segmentation algorithm to partition a given genomic sequence into isochores is put forward. The new algorithm has been applied to segment chromosomes of different organisms. The boundaries obtained by the present method are in good agreement with those of the z curve method, and also match well with the GCDT images in visualization. The present method can detect the isochore boundaries with high resolution and can be suitable for analyzing any genome sequences.

Keywords

biology computing; data visualisation; genomics; GCDT; genomic sequence; isochore boundaries; segmentation algorithm; visualization method; z curve method; Animals; Bioinformatics; Displays; Genomics; Image segmentation; Laboratories; Organisms; Partitioning algorithms; Sequences; Visualization; GC content; GCDT; genome; isochore;

fLanguage

English

Publisher

ieee

Conference_Titel

Computing, Communication, Control, and Management, 2009. CCCM 2009. ISECS International Colloquium on

Conference_Location

Sanya

Print_ISBN

978-1-4244-4247-8

Type

conf

DOI

10.1109/CCCM.2009.5270409

Filename

5270409