i-Genome: A database to summarize oligonucleotide data in genomes
1 Department of Computer Science and Information Engineering National Central University, Chung-Li 320, Taiwan
2 Department of Biological Science and Technology, Institute of Bioinformatics National Chiao Tung University, Hsin-Chu 300, Taiwan
3 Department of Biotechnology, Ming Chuan University, Taipei 111, Taiwan
4 Department of Life Science, National Central University, Chung-Li 320, Taiwan
BMC Genomics 2004, 5:78 doi:10.1186/1471-2164-5-78Published: 9 October 2004
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.
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.
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.