Scoring Matrices_5.scoring matrices .pdf
- 2. Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment. It is also known as substitution matrix. Scoring matrix of nucleotide is relatively simple
- 3. A positive value or a high score is given for a match & negative value or a low score is given for a mismatch. Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
- 6. Transition --- substitutions in which a purine (A/G) is replaced by another purine (A/G) or a pyrimidine (C/T) is replaced by another pyrimidine (C/T). Tansversions --- (A/G) (C/T)
- 8. To quantify the similarity achieved by an alignment, scoring matrices are used: They contain a value for each possible substitution, and the alignment score is the sum of the matrix's entries for each aligned amino acid pair. For gaps (indels), a special gap score is necessary---a very simple one is just to add a constant penalty score for each indel. The optimal alignment is the one which maximizes the alignment score.
- 9. An amino-acid scoring matrix is a 20x20 table such that position indexed with amino-acids so that position X,Y in the table gives the score of aligning amino-acid X with amino-acid Y
- 10. Identity matrix – Exact matches receive one score and non-exact matches a different score (“1” on the diagonal” 0” everywhere else) Mutation data matrix – a scoring matrix compiled based on observation of protein mutation rates: some mutations are observed more often then other (PAM, BLOSUM). Physical properties matrix – amino acids with with similar biophysical properties receive high score. Genetic code matrix – amino acids are scored based on similarities in the coding triple.