Global dinucleotide signatures and analysis of genomic heterogeneity
- PMID: 10066522
- DOI: 10.1016/s1369-5274(98)80095-7
Global dinucleotide signatures and analysis of genomic heterogeneity
Abstract
Early biochemical experiments measuring nearest neighbor frequencies established that the set of dinucleotide relative abundance values (dinucleotide biases) is a remarkably stable property of the DNA of an organism. Analyses of currently available genomic sequence data have extended these earlier results, showing that the dinucleotide biases evaluated for successive 50 kb segments of a genome are significantly more similar to each other than to those of sequences from more distant organisms. From this perspective, the set of dinucleotide biases constitutes a 'genomic signature' that can discriminate sequences from different organisms. The dinucleotide biases appear to reflect species-specific properties of DNA stacking energies, modification, replication, and repair mechanisms. The genomic signature is useful for detecting pathogenicity islands in bacterial genomes.
Similar articles
-
Dinucleotide relative abundance extremes: a genomic signature.Trends Genet. 1995 Jul;11(7):283-90. doi: 10.1016/s0168-9525(00)89076-9. Trends Genet. 1995. PMID: 7482779 Review.
-
Compositional biases of bacterial genomes and evolutionary implications.J Bacteriol. 1997 Jun;179(12):3899-913. doi: 10.1128/jb.179.12.3899-3913.1997. J Bacteriol. 1997. PMID: 9190805 Free PMC article.
-
Use of the genomic signature in bacterial classification and identification.Syst Appl Microbiol. 2004 Mar;27(2):175-85. doi: 10.1078/072320204322881790. Syst Appl Microbiol. 2004. PMID: 15046306
-
Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content.Gene. 2003 Jun 5;311:35-42. doi: 10.1016/s0378-1119(03)00581-x. Gene. 2003. PMID: 12853136
-
Comparative DNA analysis across diverse genomes.Annu Rev Genet. 1998;32:185-225. doi: 10.1146/annurev.genet.32.1.185. Annu Rev Genet. 1998. PMID: 9928479 Review.
Cited by
-
A beginner's guide to phylogenetics.Microb Ecol. 2013 Jul;66(1):1-4. doi: 10.1007/s00248-013-0236-x. Epub 2013 Apr 28. Microb Ecol. 2013. PMID: 23624570 Review.
-
Reconstructing horizontal gene flow network to understand prokaryotic evolution.Open Biol. 2022 Nov;12(11):220169. doi: 10.1098/rsob.220169. Epub 2022 Nov 30. Open Biol. 2022. PMID: 36446404 Free PMC article.
-
Biased distribution of DNA uptake sequences towards genome maintenance genes.Nucleic Acids Res. 2004 Feb 11;32(3):1050-8. doi: 10.1093/nar/gkh255. Print 2004. Nucleic Acids Res. 2004. PMID: 14960717 Free PMC article.
-
Identification of prophages in bacterial genomes by dinucleotide relative abundance difference.PLoS One. 2007 Nov 21;2(11):e1193. doi: 10.1371/journal.pone.0001193. PLoS One. 2007. PMID: 18030328 Free PMC article.
-
Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences.PLoS Comput Biol. 2009 Jun;5(6):e1000421. doi: 10.1371/journal.pcbi.1000421. Epub 2009 Jun 26. PLoS Comput Biol. 2009. PMID: 19557160 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
