Novel bioinformatics for inter- and intraspecies comparison of genome signatures in plant genomes

Plant Biotechnology

Volumn 26, Issue 5, 2009, Pages 469-477

  Abe, Takashi ^a   Wada, Kennosuke ^a   Iwasaki, Yuki ^a   Ikemura, Toshimichi ^a  

^a NAGAHAMA INSTITUTE OF BIO SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Batch learning SOM; Genome signature; Oligonucleotide frequency; Random sequences

Indexed keywords

EID: 76349120197     PISSN: 13424580     EISSN: 13476114     Source Type: Journal    
DOI: 10.5511/plantbiotechnology.26.469     Document Type: Article

References (33)

1. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T (2002) A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency. Genome Inform 13: 12-20.
2. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T (2003) Informatics for unveiling hidden genome signatures. Genome Res 13: 693-702.
3. Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T (2005) Novel Phylogenetic Studies of Genomic Sequence Fragments Derived from Uncultured Microbe Mixtures in Environmental and Clinical Samples. DNA Res 12: 281-290.
4. Abe T, Sugawara H, Kanaya S, Kinouchi M, Ikemura T (2006a) A large-scale Self-Organizing Map (SOM) unveils sequence characteristics of a wide range of eukaryote genomes. Gene 365: 27-34.
5. Abe T, Sugawara H, Kanaya S, Ikemura T (2006b) Sequences from almost all prokaryotic, eukaryotic, and viral genomes available could be classified according to genomes on a large-scale Self-Organizing Map constructed with the Earth Simulator. J Earth Simulator 6: 17-23.
6. Abe T, Sugawa H, Kanaya S, Kosaka Y, Ikemura T (2006c) Characterization of transcriptional regulatory signals with novel bioinformatics tools. In: Kiyama R, Shimizu M (eds) DNA structure, Chromatin and Gene Expression, Transworld Research Network, India, pp 1-16.
7. Abe T, Kanaya S, Ikemura T (2009) A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses. DNA Res 16: 287-298
8. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier, F (1985) The mosaic genome of warm-blooded vertebrates. Science 228: 953-958.
9. Bernardi, G (2004) Structural and evolutionary genomics: natural selection in genome evolution. Elsevier, Amsterdam; New York
10. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351-360.
11. Gentles AJ, Karlin S (2001) Genome-scale compositional comparisons in eukaryotes. Genome Res 11: 540-546.
12. Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucl Acids Res 8: r49-r62
13. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2: 13-34.
14. Ikemura T, Aota S (1988) Global variation in G C content along vertebrate genome DNA. Possible correlation with chromosome band structures. J Mol Biol 203: 1-13.
15. Hayashi H, Abe T, Sakamoto M, Ohara H, Ikemura T, Sakka K, Benno Y (2005) Direct cloning of genes encoding novel xylanases from human gut. Can J Microbiol 51: 251-259.
16. Kanaya S, Kudo Y, Nakamura Y, Ikemura T (1996) Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage. CABIOS 12: 213-225.
17. Kanaya S, Kudo Y, Abe T, Okazaki T, Carlos DC, Ikemura T (1998) Gene classification by self-organization mapping of codon usage in bacteria with completely sequenced genome. Genome Inform 9: 369-371.
18. Kanaya S, Yamada Y, Kudo Y, Ikemura T (1999) Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238: 143-155.
19. Kanaya S, Kinouchi M, Abe T, Kudo Y, Yamada Y, Nshi T, Mori H, Ikemura T (2001) Analysis of codon usage diversity of bacterial genes with a self-organizing map: characterization of horizontally transferred genes with emphasis on E. coli O157 genome. Gene 276: 89-99.
20. Karlin S, Mrazek J, Campbell A (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179: 3899-3913.
21. Karlin S (1998a) Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1: 598-610.
22. Karlin S, Campbell A, Mrazek, J (1998b) Comparative DNA analysis across diverse genomes. Annu Rev Genet 32: 185-225.
23. Kohonen T (1982) Self-organized formation of topologically correct feature maps. Biol Cybern 43: 59-69.
24. Kohonen T (1990) The self-organizing map. Proc IEEE 78: 1464-1480
25. Kohonen T, Oja E, Simula O, Visa A, Kangas J (1996) Engineering applications of the self-organizing map. Proc IEEE 84: 1358-1384
26. Nussinov R (1984) Doublet frequencies in evolutionary distinct groups. Nucl Acids Res 12: 1749-1763.
27. Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ (2003) Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 13: 145-158.
28. Rocha EP, Viari A, Danchin A (1998) Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucl Acids Res 26: 2971-2980.
29. Sharp PM, Matassi G (1994) Codon usage and genome evolution. Curr Opin Gen Dev 4: 851-860.
30. Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate- induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23: 88-93.
31. Yamamoto YY, Ichida H, Abe T, Suzuki Y, Sugano S, Obokata J (2007a) Differentitation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucl Acid Res 35: 6219-6226.
32. Yamamoto YY, Ichida H, Matui M, Obokata J, Sakurai T, Satou M, Seki M, Shinozaki K, Abe T (2007b) Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics 8: 67
33. Zhang R, Zhang CT (2004) Isohore structures in the genome of the Plant Arabidopsis thaliana. J Mol Evol 59: 227-238