Fundamentals of Bioinformatics - Ourtsov, A.N. 2013

Methods of Bioinformatics Analysis
Substitution Matrices
Calculating Sequence Alignment Scores

Let us examine the Procedure for calculating an alignment score using two sequences as an example:

1) human alpha-globin HBA_HUMAN

Class="center">

2) yellow lupine leghemoglobin LGB2_LUPLU

Using the BLOSUM50 matrix (Table 13) and an affine gap penalty y(g) = -d - (g - 1)e, let us calculate the score S1 for the following alignment fragment with d = 12 and e = 2

of the human alpha-globin fragment

and the corresponding yellow lupine leghemoglobin fragment

The total score of any alignment is the sum of substitution scores for the aligned Amino Acids and gap penalties determined by the formula y(g) = -12 - (g - 1) ∙ 2, where g is the gap length. In this case, we obtain

Under the same conditions, let us calculate the score S₂ for the alignment of the human alpha-globin fragment HBA_HUMAN and the corresponding nematode Glutathione S-transferase fragment GST7_CAEEL

Consider the following alignment fragment

We obtain

The alignment of these two pairs of sequence fragments showed that the structurally and evolutionarily plausible alignment of human alpha-globin with leghemoglobin (the first alignment) received a lower score than the alignment of human alpha-globin with the unrelated nematode protein sequence (the second alignment). This example highlights Structure/19.html">The Importance of expert, biologically meaningful evaluation when inferring Homology based on computational analysis.

The same scores, but for other BLOSUM Matrices (Tables 12, 14, 15), will appear as follows

METABOLISM/35.html">Selection/41.html">Review Questions and Assignments

1. What are the two Methods for quantitatively measuring the distance between two given sequence strings?

2. What are the types of deletion penalties?

3. WHAT IS A PAM matrix?

4. What does a sequence distance of 1 PAM correspond to?

5. Show what the mutation probability of the V↔M substitution is equal to, if the corresponding mutation cost in the PAM250 matrix is

6. What is the difference between the construction principles of BLOSUM and PAM Matrices?

7. To align the human Hemoglobin alpha subunit HBA_HUMAN with Danio rerio cytoglobin-1 using the PAM30 matrix and an affine gap penalty y(g) = -d - (g - 1)e (with d = 10 and e = 5), calculate the score of the following alignment fragment

8. To align the human hemoglobin alpha subunit HBA_HUMAN with Danio rerio cytoglobin-1 using the BLOSUM80 matrix and an affine gap penalty y(g) = -d - (g - 1)e (with d = 8 and e = 4), calculate the score of the following alignment fragment