Sequence allignment The optimum cost of an alignment of the strings x1 x2 x3 x4

Question

Sequence allignment

The optimum cost of an alignment of the strings

x1 x2 x3 x4 ... x_m and y1 y2 y3 ... y_n

will always be greater than the optimum cost of an alignment of

   x2 x3 x4 ... x_m and y1 y2 y3 ... y_n

because any alignment of the first pair of strings necessarily contains an alignment of the second pair of strings.

This is NOT correct!

It is NOT true that any alignment of the first pair of strings necessarily contains an alignment of the second pair of strings: For example, let x = CT and let y = CG. It is NOT true that any alignment of these start with x1 = C against a gap, followed by an alignment of x2 against y1 y2 (i.e., an alignment of T against CG). Here is such an alignment:

A T
A G

This alignment has cost 1, whereas any alignment that starts with the first A in x against a gap necessarily will have cost at least 2 for that first gap, and optimally has cost 5:

A T -
- A G

Is it possible to have a situation in table "opt" where x_i is the same character as y_j and have

opt[ i ][ j ] = 2 + opt[ i+1][ j ] = 2 + opt[ i ][ j+1]    = 0 + opt[ i + 1][ j + 1]

(In other words, when creating the alignment, we could have come from ANY of the 3 neighboring squares below and to the right?

You need to compute the entire "opt" table, and see if there exists an i and a j such that x_i == y_j and when you are computing the value of opt[i][j], it is a 3-way tie between 2+opt[i + 1][j], 2+opt[i][j + 1], and opt[i+1][j+1].

Explanation / Answer

calculate the grade of a student on the basis of his/her total marks in Java programming, you have to ask to the user to enter the marks obtained in some subjects (5 subjects here), then calculate the percentage and start checking for the grades to display the grade on the output screen.

Java Programming Code to Calculate Grade

Following program ask to the user to enter the marks obtained in 5 subjects to calculate and display the grade of student:

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