Abstract
Concepts and methods [Karlin, S. & Ghandour, G. (1985) Proc. Natl. Acad. Sci. USA 82, 5800-5804] for the analysis of patterns and relationships are extended to multiple DNA and protein sequences. Functionals include multiple sequence common word occurrence distributions, characterizations of high frequency shared words, and ascertainment of long block identities. Various comparisons of sequences using natural alphabets obtained from grouping nucleotides or amino acids by their chemical and functional characteristics are described. Specific applications are given to globin genes, mitochondrial genomes, and a variety of mammalian viruses.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Early P., Huang H., Davis M., Calame K., Hood L. An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH. Cell. 1980 Apr;19(4):981–992. doi: 10.1016/0092-8674(80)90089-6. [DOI] [PubMed] [Google Scholar]
- Efstratiadis A., Posakony J. W., Maniatis T., Lawn R. M., O'Connell C., Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M., Slightom J. L. The structure and evolution of the human beta-globin gene family. Cell. 1980 Oct;21(3):653–668. doi: 10.1016/0092-8674(80)90429-8. [DOI] [PubMed] [Google Scholar]
- Haber J. E., Koshland D. E., Jr An evaluation of the relatedness of proteins based on comparison of amino acid sequences. J Mol Biol. 1970 Jun 28;50(3):617–639. doi: 10.1016/0022-2836(70)90089-6. [DOI] [PubMed] [Google Scholar]
- Hardison R. C. Comparison of the beta-like globin gene families of rabbits and humans indicates that the gene cluster 5'-epsilon-gamma-delta-beta-3' predates the mammalian radiation. Mol Biol Evol. 1984 Sep;1(5):390–410. doi: 10.1093/oxfordjournals.molbev.a040326. [DOI] [PubMed] [Google Scholar]
- Hardison R. C., Margot J. B. Rabbit globin pseudogene psi beta 2 is a hybrid of delta- and beta-globin gene sequences. Mol Biol Evol. 1984 Jul;1(4):302–316. doi: 10.1093/oxfordjournals.molbev.a040321. [DOI] [PubMed] [Google Scholar]
- Hieter P. A., Max E. E., Seidman J. G., Maizel J. V., Jr, Leder P. Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments. Cell. 1980 Nov;22(1 Pt 1):197–207. doi: 10.1016/0092-8674(80)90168-3. [DOI] [PubMed] [Google Scholar]
- Karlin S., Ghandour G. Alignment maps and homology analysis of the J-C intron in human, mouse, and rabbit immunoglobulin kappa gene. Mol Biol Evol. 1985 Jan;2(1):53–65. doi: 10.1093/oxfordjournals.molbev.a040337. [DOI] [PubMed] [Google Scholar]
- Karlin S., Ghandour G. Comparative statistics for DNA and protein sequences: single sequence analysis. Proc Natl Acad Sci U S A. 1985 Sep;82(17):5800–5804. doi: 10.1073/pnas.82.17.5800. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Karlin S., Ghandour G., Foulser D. E. DNA sequence comparisons of the human, mouse, and rabbit immunoglobulin kappa gene. Mol Biol Evol. 1985 Jan;2(1):35–52. doi: 10.1093/oxfordjournals.molbev.a040336. [DOI] [PubMed] [Google Scholar]
- Karlin S., Ghandour G., Foulser D. E., Korn L. J. Comparative analysis of human and bovine papillomaviruses. Mol Biol Evol. 1984 Jul;1(4):357–370. doi: 10.1093/oxfordjournals.molbev.a040318. [DOI] [PubMed] [Google Scholar]
- Karlin S., Ghandour G. The use of multiple alphabets in kappa-gene immunoglobulin DNA sequence comparisons. EMBO J. 1985 May;4(5):1217–1223. doi: 10.1002/j.1460-2075.1985.tb03763.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McLachlan A. D. Repeating sequences and gene duplication in proteins. J Mol Biol. 1972 Mar 14;64(2):417–437. doi: 10.1016/0022-2836(72)90508-6. [DOI] [PubMed] [Google Scholar]
- Miyata T., Miyazawa S., Yasunaga T. Two types of amino acid substitutions in protein evolution. J Mol Evol. 1979 Mar 15;12(3):219–236. doi: 10.1007/BF01732340. [DOI] [PubMed] [Google Scholar]