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Bioinformatics Vol. 19 no. 5 2003
Pages 593-599
© 2003 Oxford University Press

The Z curve database: a graphic representation of genome sequences

Chun-Ting Zhang 1,*, Ren Zhang 2 and Hong-Yu Ou 1

1 Department of Physics, Tianjin University, Tianjin 300072, People's Republic of China
2 Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, People's Republic of China

Received on July 11, 2002 ; revised on September 12, 2002 and October 26, 2002 ; accepted on November 11, 2002

Motivation: Genome projects for many prokaryotic and eukaryotic species have been completed and more new genome projects are being underway currently. The availability of a large number of genomic sequences for researchers creates a need to find graphic tools to study genomes in a perceivable form. The Z curve is one of such tools available for visualizing genomes. The Z curve is a unique three-dimensional curve representation for a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z curve database for more than 1000 genomes have been established here.

Results: The database contains the Z curves for archaea, bacteria, eukaryota, organelles, phages, plasmids, viroids and viruses, whose genomic sequences are currently available. All the 3-dimensional Z curves and their three component curves are stored in the database. The applications of the Z curve database on comparative genomics, gene prediction, computation of G+C content with a windowless technique, prediction of replication origins and terminations of bacterial and archaeal genomes and study of local deviations from the Chargaff Parity Rule 2 etc. are presented in detail. The Z curve database reported here is a treasure trove in which biologists could find useful biological knowledge.

Availability: The Z curve database is freely available at the website: http://tubic.tju.edu.cn/zcurve/

Contact: ctzhang{at}tju.edu.cn

* To whom correspondence should be addressed.


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