Sequencing alignment

Fig. 10.12 Sequence alignment of trypsin, chymotrypsin and thrombin (bovine). The active sites histidine, aspartic acid and serine are highlighted.

Fig. 10.16 Finding the optimal sequence alignment using dynamic programming with a scoring scheme in which a match scores 1, a mismatch scores —1 and the gap penalty is —2.

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.

A sequence alignment establishes the correspondences between the amino adds in th unknown protein and the template protein (or proteins) from wliich it will be built. Th three-dimensional structures of two or more related proteins are conveniently divided int structurally conserved regions (SCRs) and structurally variable regions (SVRs). Ihe structural conserved regions correspond to those stretches of maximum sequence identity or sequenc... 

Dynamic programming Technique widely used in sequence alignment... 

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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 ... 

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