The use of sequence comparison to detect 'identities' in tRNA genes
| Autor: | Jun-Ichi Sagara, Mitsunori Ikeguchi, Takeshi Kawabata, Kentaro Shimizu, Seishi Shimizu, Shugo Nakamura |
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| Rok vydání: | 1998 |
| Předmět: |
DNA
Bacterial Models Molecular RNA Transfer Leu Molecular Sequence Data Sequence alignment Computational biology Biology Amino Acyl-tRNA Synthetases RNA Transfer Pro RNA Transfer RNA Transfer Gln Sequence Homology Nucleic Acid Sequence comparison Anticodon Escherichia coli Genetics Gene Base Sequence Group (mathematics) RNA Bacterial Order (biology) Genes Bacterial Transfer RNA Principal component analysis Nucleic Acid Conformation Sequence Alignment Research Article |
| Zdroj: | Nucleic Acids Research. 26:1974-1979 |
| ISSN: | 1362-4962 |
| DOI: | 10.1093/nar/26.8.1974 |
| Popis: | We have developed a computational method that detects 'identities' in tRNA genes by using principal component analysis to classify the sequences of bases in tRNA genes into groups of similar sequences and then comparing the distribution of sequences of bases, in order to extract characteristic bases that are conserved within a group but differ between groups. These classification and comparison procedures are applied recursively to classify the sequences into hierarchical groups, so that multiple levels of characteristic sites can be detected. By using this computational method, we were able to detect many characteristic sites in the T and D domains of tRNAs, as well as the characteristic sites that had already been detected experimentally. This suggests that bases not only in the contact regions but also in the elbow regions, which determine the structure and dynamics of the whole tRNA molecule, are important to the tRNA-aminoacyl tRNA synthetase recognition. |
| Databáze: | OpenAIRE |
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