Indian Computing Olympiad

Training Material

Dynamic Programming→DNA (APIO 2008)

One interesting use of computer is to analyze biological data such as DNA sequences. Biologically, a strand of DNA is a chain of nucleotides Adenine, Cytosine, Guanine, and Thymine. The four nucleotides are represented by characters A, C, G, and T, respectively. Thus, a strand of DNA can be represented by a string of these four characters. We call such a string a DNA sequence.

It is possible that the biologists cannot determine some nucleotides in a DNA strand. In such a case, the character N is used to represent an unknown nucleotides in the DNA sequence of the strand. In other words, N is a wildcard character for any one character among A, C, G or T. We call a DNA sequence with one or more character N an incomplete sequence ; otherwise, it is called a complete sequence. A complete sequence is said to agree with an incomplete sequence if it is a result of substituting each N in the incomplete sequence with one of the four nucleotides. For example, ACCCT agrees with ACNNT, but AGGAT does not.

Researchers often order the four nucleotides the way we order the English alphabets: A comes before C, C comes before G, G comes before T. A DNA sequence is classified as form-1 if every nucleotide in it is the same as or comes before the nucleotides immediately to its right. For example, AACCGT is form-1, but AACGTC is not.

In general, a sequence is form-j , for j>1, if it is a form-(j-1) or it is a concatenation of a form-(j-1) sequence and a form-1 sequence. For example, AACCC, ACACC, and ACACA are form-3, but GCACAC and ACACACA are not.

Again, researchers order DNA sequences lexicographically the way we order words in a dictionary. As such, the first form-3 sequence of length 5 is AAAAA, and the last is TTTTT. As another example, consider the incomplete sequence ACANNCNNG. The first seven form-3 sequences that agree with it are:


Given an incomplete sequence of length M, and two values K and R, the task to find the Rth form-K sequence that agrees with the given incomplete sequence.

Here M≤50000, K≤10, R≤212.