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Home > Problems > Chapter 5
3. When a global msa can be made, one can pick out the most conserved regions (motifs), make a scoring matrix, and search for other sequences that have this same motif. The matrix will take into account the variation found in the sequences. We will make a position-specific scoring matrix (PSSM, also called a scoring matrix, or weight matrix) by hand corresponding to a short msa and then use the matrix to scan a sequence. Here is a table showing the frequency of each base in an alignment that is four bases long:
- Assuming that the background frequency is 0.25 for each base, calculate a log odds score for each table position; i.e., log to the base 2 of the ratio of each observed value to the expected frequency.
- Align the matrix with each position in the sequence TGAGCTAA starting at position 1, 2, etc., and calculate the log odds score for the matrix to match that position.
- Now convert the alignment scores to ODDS scores, sum them, and calculate the probability of the best matching position.
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