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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:
  1. 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.
  2. 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.
  3. Now convert the alignment scores to ODDS scores, sum them, and calculate the probability of the best matching position.


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