Multiple sequences

Fig. 10.20 Schematic illustration of the creation of a multiple sequence alignment for five sequences A-E. In the fi step sequences C and E are aligned. In the second step sequences A and D are aligned. In the third step the pair Cl aligned with the pair AD. Finally, the quartet CEAD is aligned with B.

Cuff IA and G J Barton 1999. Evaluation and Improvement of Multiple Sequence Methods for P Secondary Structure Prediction. Proteins Structure, Function and Genetics 34 508-519. 

Ortiz A R, A Kolinski and J Skolnick 1998. Fold Assembly of Small Proteins Using Monte C Simulations Driven by Restraints Derived from Multiple Sequence Alignments. Jourru Molecular Biology 277 419-446. 

AD Baxevams. Pi actical aspects of multiple sequence alignment. Methods Biochem Anal 39 172-188, 1998. 

E Jeanmougm, JD Thompson, M Gouy, DG Eliggms, TJ Gibson. Multiple sequence alignment with clustal X. Trends Biochem Sci 23 403-405, 1998. 

WR Taylor, K Hatrick. Compensating changes m protein multiple sequence alignments. Protein Eng 7 341-348, 1994. 

AR Ortiz, A Kolinski, J Skolnick. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 277 419-448, 1998. 

CX.0 = Z(=iCx.r represents the total number of counts that the prior distribution represents, and the a, the counts for each type of amino acid (not necessarily integers). Because different distributions will occur in multiple sequence alignments, the prior distribution for any position should be represented as a mixture of N Dirichlet distributions ... 

Sjdlander et al. [16] describe the process assumed in their model of sequence alignments, which is how the counts for a particular position in a multiple sequence alignment would arise from the mixture Dirichlet prior ... 

Thompson and Goldstein [89] improve on the calculations of Stolorz et al. by including the secondary structure of the entire window rather than just a central position and then sum over all secondary strucmre segment types with a particular secondary structure at the central position to achieve a prediction for this position. They also use information from multiple sequence alignments of proteins to improve secondary structure prediction. They use Bayes rule to fonnulate expressions for the probability of secondary structures, given a multiple alignment. Their work describes what is essentially a sophisticated prior distribution for 6 i(X), where X is a matrix of residue counts in a multiple alignment in a window about a central position. The PDB data are used to form this prior, which is used as the predictive distribution. No posterior is calculated with posterior = prior X likelihood. 

TR Defay, EE Cohen. Multiple sequence information for threading algorithms. J Mol Biol 262 314-323, 1996. 

WR Taylor. Multiple sequence threading An analysis of alignment quality and stability. J Mol Biol 269 902-943, 1997. 

Families of similar sequences contain information on sequence evolution in the form of specific conservation patterns at all sequence positions. Multiple sequence alignments are useful for... 

This branch of bioinformatics is concerned with computational approaches to predict and analyse the spatial structure of proteins and nucleic acids. Whereas in many cases the primary sequence uniquely specifies the 3D structure, the specific rules are not well understood, and the protein folding problem remains largely unsolved. Some aspects of protein structure can already be predicted from amino acid content. Secondary structure can be deduced from the primary sequence with statistics or neural networks. When using a multiple sequence alignment, secondary structure can be predicted with an accuracy above 70%. 

An interesting combination of enzymatic with non-enzymatic transformation in a one-pot three-step multiple sequence was reported by Waldmann and coworkers [82]. Phenols 125 in the presence of oxygen and enzyme tyrosinase are hydroxylated to catechols 126 which are then oxidized in situ to ortho quinones 127. These intermediates subsequently undergo a Diels-Alder reaction with inverse electron demand by reaction with different dienophiles (Table 4.19) to give endo bicyclic 1,2-diketones 128 and 129 in good yields. 

Like most viral RNA polymerases, NS5B does not possess 3 -5 exonuclease editing capability and is relatively error prone. This results in a mutation rate of approximately 1.4 x 10 nucleotide changes per site per year [18, 19]. Combined with the estimated production of up to 10 virions per day in an infected individual [20], HCV sequences clearly have the potential to evolve rapidly. This results in the appearance of multiple sequence variants or quasi-species in each infected individual [21]. 

Hoffmeyer, S., Burk, O., von Richter, O., Arnold, H. P., Brockmoller, J., Johne, A., Cascorbi, I., Gerlo, T., Roots, I., Eichelbaum, M., Brinkmann, U., Functional polymorphism of the human multidrug resistance gene multiple sequence variations and correlation of one allele with P-glycoprotein expression and activity in vivo, Proc. Natl. Acad. Sci. USA 2000, 97, 3473-3478. 

The other subfamily, SLC1, includes the Na+-dependent glutamate transporters. It encompasses some amino- and carboxylic-acid transporters including glutamate transporters that are expressed in bacteria. X-ray diffraction data have been obtained from crystals of one of these [43] (Fig. 5-13). Analysis of multiple sequence alignments indicates that this molecule has a high degree of structural... 

Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G. The CLUSTAL X windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 4876-4882, 1997. 

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