Molecular sequence

SF Altschul, MS Boguski, W Gish, JC Wootton. Issues in searching molecular sequence databases. Nature Genet 6 119-129, 1994. 

In addition to the multiple processes involving two Diels-Alder reactions in intra-intra, inter-intra or inter-inter molecular sequences, other processes have... 

A mechanism of action describes the molecular sequence of events (covalent or non-covalent) that lead to the manifestation of a response. The complete elucidation of the reactions and interactions among and between chemicals, include very complex and varied situations including biological systems (macromolecular receptors, physical phenomena (thermodynamics of explosions) or global systems (ozone depletion). Unfortunately, this level of mechanistic detail is often unavailable but recent advances in molecular toxicology and others hazards, at the molecular level, have provided valuable information that elucidates key steps in a mechanism or mode of action. ... 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

Karlin, S., and Altschul, S. F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87, 2264-2268. 

Waterman, M. S. in Mathematical and Computational Problems in the Analysis of Molecular Sequences Bull. Math. Biol. 1984, 46) Pergamon Oxford, 1984 p. 473. Cf. other articles in this volume. 

Arisue N, Hasegawa M, Hashimoto T (2005) Root of the eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol Biol Evol 22 409-420... 

The mechanisms underlying glutamate and its analog-induced neuronal damage are quite complex. The molecular sequence of these events is not fully understood. The mechanisms include inhibition of mitochondrial function and increases... 

Fig. 28. Molecular structure of the ttgg crystal form of sPP. a and b show the relationship between the methylene and methine carbons separated by three bonds, in trans (a) and gauche (b). c shows the side view and the view from the c axis of the molecular sequence in the ttgg crystal form. The closed and open circles in the main chain show the methylene and methine carbons, respectively. The methylene carbons marked as A and B are the methylene carbon with two gauche effects (the gt-gt carbon) and that without gauche effect (the tg-gt carbon), respectively. See the text...

Molecular structures do not redraw the Darwinian tree of evolution but rather the clonal distribution of the Genomic Potential Hypothesis, and that forces us to realize that the model of descent with variation cannot be correct. Instead one observes clusters within clusters, both, in taxon development and molecular sequence similarity. One sees parallel world lines of proteins and species evolving as if from nothing, at different levels in antiquity, ending in extinction or breaking the surface to the present. 

Types I, II, and III collagen form the fibrous network that prevents premature mechanical failure of most tissues and acts to transmit stress to and from cells. The molecular sequences of these collagens are known and they are composed of approximately 1000 amino acids in the form of Gly-X-Y with small nonhelical ends before and after these sequences. All of these collagen types form continuous triple-helical structures that pack laterally... 

Microsporidia had also lost their mitochondria and their ancient status too (Germot et al. 1997). They were found to have had unusual molecular sequences resulting from their parasitic lifestyle that led them to be misplaced in RNA-based phylogenetic trees. Rather than being at the bottom, they were actually at the crown with the fungi (Hirt et al. 1999). 

Gupta R (2005) Molecular sequences and the early history of life. In Sapp J (ed) Microbial phylogeny and evolution concepts and controversies. Oxford University Press, New York, pp 160-183... 

Arisue N, Hashimoto T, Yoshikawa H, Nakamura Y, Nakamura G, Nakamura F, Yano TA, Hasegawa M (2002c) Phylogenetic position of Blastocystis hominis and of stramenopiles inferred from multiple molecular sequence data. J Eukaryot Microbiol 49 42-53... 

Cladistic analysis of molecular sequence characters differs from that described by Hennig17 for organismal characters in several important ways. Molecules do not leave fossils, thus there is no hard record of which character state (i.e., amino acid residue) is ancestral and which is derived at any position in a sequence. The 20 common amino acids are found in all living forms and therefore have nothing inherently ancestral or derived about them. Furthermore, amino acid replacements have no intrinsic directionality, even though some replacements are more likely to occur than others. In other words, amino add replacements are not inherently polarized. In addition, amino acid replacements and nucleotide substitutions are reversible. For these reasons, the character state(s) of the outgroup molecule(s) cannot be assumed to be ancestral. 

Segmented thermoplastic elastomers exhibit structural heterogeneity on the molecular, the domain, and in some cases on a larger scale involving periodic or spherulitic texture. Each level of structural organization is studied by specific methods. Molecular sequence distributions can be studied by chemical methods, such as NMR or IR spectroscopy. 

Mechanism of action The molecular sequence of events from absorption of an effective dose to production of a specific biological response. 

Doolittle, R. F. (1996). Computer Methods for Macro-molecular Sequence Analysis. Methods Enzymology, 266. 

Artificial neural networks are now widely used to solve various problems in genome informatics and molecular sequence analysis. Part III provides an in-depth discussion of special system designs and considerations for building neural networks for genome informatics applications (chapters 6-8), and broad reviews of state-of-the-art methods and their evaluations (chapters 9-11). 

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