BLOSUM matrices

Figure 6.11 Alignment of identities only versus the Blosum 62 matrix. Repeated shuffling and scoring reveal the significance of sequence alignment for human myoglobin versus lupine leghemoglobin with the use of either (A) the simple, identity-based scoring system or (B) the Blosum-62 matrix. The scores for the alignment of the authentic sequences are shown in red. The Blosum matrix provides greater statistical power.

Fig. 4. Substitution matrix based on disordered protein families. Below the diagonal are the scores for each amino acid substitution. Above the diagonal are the differences between BLOSUM 62 and the disorder matrix. On the diagonal are the scores/differences. (From Radivojac et al., 2002, PSB 2002 7, 589-600, with permission of World Scientific Publishing Co. Pte Ltd.)...

Fig. 2. The BLOSUM 50 substitution matrix (Henikoff and Henikoff, 1992) lower) and the difference matrix upper) obtained by subtracting it from the Gonnet matrix (Gonnet et al., 1992) position by position.

From the examination of appropriately aligned sequences, substitution matrices can be deduced. In these matrices, a large positive score corresponds to a substitution that occurs relatively frequently, whereas a large negative score corresponds to a substitution that occurs only rarely. The Blosum-62 substitution matrix illustrated in Figure 7 9 is an example. The highest scores in this substitution matrix indicate that amino acids such as cysteine (C) and tryptophan (W) tend to be conserved more than those such as serine (S) and alanine (A). Furthermore, structurally conservative... 

Figure 7.12. Alignment of Human Myoglobin and Lupine Leghemoglobin. The use of the Blosum-62 substitution matrix yields the alignment shown between human myoglobin and lupine leghemoglobin, illustrating identities (orange) and conservative substitutions (yellow). These sequences are 23% identical.

Which alignment has a higher score if the identity-based scoring system (Section 7.2) is used Which alignment has a higher score if the Blosum-62 substitution matrix (Figure 7.9) is used ... 

FIGURE 7.11 Alignment of identities only versus the Blosum 62 matrix. 

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