The Z curve database: a graphic representation of genome sequences.
BACKGROUND
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.
Zhang
Chun-Ting
CT
Department of Physics, Tianjin University, Tianjin 300072, People's Republic of China. ctzhang@tju.edu.cn
Zhang
Ren
R
Ou
Hong-Yu
HY
D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D016678:Genome; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D004247:DNA