i-Genome: a database to summarize oligonucleotide data in genomes.
BACKGROUND
Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming.


RESULTS
The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes.


CONCLUSIONS
This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.
Lin
Feng-Mao
FM
Department of Computer Science and Information Engineering National Central University, Chung-Li 320, Taiwan. meta@db.csie.ncu.edu.tw <meta@db.csie.ncu.edu.tw>
Huang
Hsien-Da
HD
Chang
Yu-Chung
YC
Horng
Jorng-Tzong
JT
D020087:Alu Elements / Q000235:genetics; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D030541:Databases, Genetic; D016678:Genome; D016680:Genome, Bacterial; D016681:Genome, Fungal; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics; D009841:Oligonucleotides / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics; D020079:Terminal Repeat Sequences / Q000235:genetics
D009841:Oligonucleotides