Step 2 Sequence Alignment

Most sequence alignment methods are automated, but some are performed manually. Both the automated and the manual alignment of multiple chains is a challenging problem because of the myriad of alignment possibilities. The number of combinations for alignment is determined by raising the number of sequences by the number of amino acid residues of the longest sequence (Equation [1]). 

The alignment of two sequences with 150 residues thus has more than 1.42 X 10 possible configurations, as an example. 

The goal of automated alignment methods is to align multiple protein sequences correctly with minimal user input. Although the alignment parameters are selected by the user, they are typically the well-established similar- 

Similarity matrices are mathematical representations describing the probability of a specific amino acid residue mutating to a different residue type. The alignment programs discussed in this section differ from one another by the methods they use to align the sequences. Very similar (closely related) sequences can be quickly and aptly aligned. However, as the sequences become more distantly related based on evolution, the ability of the alignment methods deteriorates. 

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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.

FIGURE 12.19 Steps in the thermal denaturation and renaturation ofDNA. The nucle-ation phase of the reaction is a second-order process depending on sequence alignment of the two strands. This process takes place slowly because it takes time for complementary sequences to encounter one another in solution and then align themselves in register. Once the sequences are aligned, the strands zipper up quickly. 

Correction of the sequence alignment based on die evaluation of the model Iteration of the last three steps... 

Repeat steps 5 and 6 until the desired results or convergence (see Notes 6 and 7). E. coli DNA polymerase III (3-subunit protein encoded by the dnaN gene is retrieved in the fifth iteration and the sequence alignment that is obtained is shown in Fig. 2. 

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