Nucleotide sequencing comparison

Nucleotide sequence comparison can be carried out on portions of the genome rather than the entire genome. The chosen portions correspond with essential functions, common to the strains to be... 

Figure 9.3 Comparison of the consensus nucleotide sequence of the TATA box (a) and the sequences of the DNA fragments used in the crystal structure determinations of the TATA box-binding proteins from yeast (b) and the plant Arabidopsis thaliana (c).

If a phylogenetic comparison is made of the 16S-Iike rRNAs from an archae-bacterium Halobacterium volcanii), a eubacterium E. coli), and a eukaryote (the yeast Saccharomyces cerevisiae), a striking similarity in secondary structure emerges (Figure 12.40). Remarkably, these secondary structures are similar despite the fact that the nucleotide sequences of these rRNAs themselves exhibit a low degree of similarity. Apparently, evolution is acting at the level of rRNA secondary structure, not rRNA nucleotide sequence. Similar conserved folding patterns are seen for the 23S-Iike and 5S-Iike rRNAs that reside in the... 

Johnston, T. C., et al. (1990). The nucleotide sequence of the luxA and luxB genes of Xenorhabdus luminescence HM and a comparison of the amino acid sequences of luciferases from four species of bioluminescent bacteria. Biochem. Biophys. Res. Commun. 170 407- 115. 

The agreement between the values predicted by the two methods is very good except in the number of sites at high exposures. The experimentally measured quantity for hydrates was not just H because the nucleotide sequence DH was not split by the enzymes employed. The number required from the calculations then was not H but XH which is the number of H s which do not have D to the left of them. Sequences such as this, and others, could be calculated by either method. The growth curves of such sequences with exposure could therefore be calculated. Comparisons of such calculations with experiment will also be given later. 

The structure of the mSos protein (m=mammalian) is shown in Fig. 9.8. Sequence comparison with known Ras-specific GEFs has identified a common domain of ca.200 amino acids, to which nucleotide exchange activity has been assigned. Within this domain, three highly conserved sequence elements can be differentiated, separated by more variable sections. Other structural elements include a PH domain and a Pro-rich binding domain. The Pro-rich sequence fimctions as an attachment site for the SH3 group of Grb2 protein. 

Ellis JE, Yarlett N, Cole D, Humphreys MJ, Lloyd D (1994) Antioxidant defenses in the microaerophilic protozoan Trichomonas vaginalis—comparison of metronidazole-resistant and sensitive strains. Microbiol-SGM 140 2489-2494 Haggoud A, Reysset G, Azeddoug H, Sebald M (1994) Nucleotide sequence analysis of two 5-nitroimidazole resistance determinants from Bacterioides strains and of a new insertion sequence upstream of the two genes. Antimicrob Agents Chemother 38 1047-1051... 

Ishida, N., Ueda, S., Hayashida, H., Miyata, T., Honjo, T. (1982). The nucleotide sequence of the mouse immunoglobulin epsilon gene comparison with the human epsilon gene sequence. EMBO J. 1, 1117-1123. 

A map showing the position of cut sites for a variety of restriction enzymes is called the restriction map for that DNA molecule. Restriction maps allow comparison between DNA molecules without the need to determine the nucleotide sequence and are also much used in recombinant DNA experiments. 

The sugars and phosphates are omitted in this notation. A comparison of DNA sequences comparison allows one to determine the relationship between different organisms and is also used to find small differences in humans (so-called DNA fingerprinting), see also Nucleic Acids Nucleotide Ribonucleic Acid. 

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