Scoring schemes in bioinformatics
- 2. CONTENT INTRODUCTION TO SCORING SCHEMES PAM-PERCENT ACCEPTED MUTATION CONSTRUCTION OF PAM SCORES IN PAM MATRICES PAM MATRICES’ NUMBERS MORE ABOUT PAM MATRICES REFERENCES
- 3. INTRODUCTION TO SCORING SCHEMES Scoring system is a set of values for quantifying the likelihood of one residue being substituted by another in an alignment. The scoring systems are called substitution matrices which account for residue identity, substitutions, and insertions or deletions. These are derived from statistical analysis of residue substitution data from sets of reliable alignments of highly related sequences. Two popular empirical scoring models for protein sequences are: PAM and BLOSUM
- 4. INTRODUCTION TO SCORING SCHEMES(cont.) In molecular biology scores are defined as measures of sequence similarity. Similar sequences give high scores and dissimilar sequences give low scores. Deletions, or gaps in a sequence, will have scores that depend upon their lengths.
- 5. PAM-PERCENT ACCEPTED MUTATION Margaret Dayhoff and coworkers originally proposed PAM model of evolution in the 60’s. 'Accepted' means fixed in the population and is therefore a more complex process than simply mutation. A point accepted mutation - is the replacement of a single amino acid in the primary structure of a protein with another single amino acid, which is accepted by the processes of natural selection. This definition does not include all point mutations in the DNA of an organism. In particular, silent mutations are not point accepted mutations, nor are mutations which are lethal or which are rejected by natural selection in other ways.
- 6. PAM-PERCENT ACCEPTED MUTATION(cont.) 'PAM matrix' refers to one of a family of matrices which contain scores representing the likelihood of two amino acids being aligned due to a series of mutation events, rather than due to random chance. 'PAMn matrix' is the PAM matrix corresponding to a time frame long enough for ‘n' mutation events to occur per 100 amino acids. Here each column and row represents one of the twenty standard amino acids. The value in each cell of a PAM matrix is related to the probability of a row amino acid before the mutation being aligned with a column amino acid afterwards. Different PAM matrices correspond to different lengths of time in the evolution of the protein sequence
- 7. CONSTRUCTION OF PAM Construction of PAM1 matrix involves alignment of full length sequences and clustering based on phylogenetic reconstruction using parsimony principle. The other PAM matrices are subsequently derived based on the evolutionary divergence between sequences of the same cluster. This allows computation of ancestral sequence for each internal node of the trees. This information in turn is used to count the number of substitution along each branch of tree.
- 8. CONSTRUCTION OF PAM (cont.) The PAM score for a particular residue pair is derived from a multistep procedure involving calculations of relative mutability which is:- 1. The number of mutational changes from a common ancestor for a particular amino acid residue divided by the total number of such residues occurring in an alignment. 2. Normalization of the expected residue substitution frequencies by random chance, 3. and logarithmic transformation to the base of 10 of the normalized mutability value divided by the frequency of a particular residue. The resulting value is rounded to the nearest integer and entered into the substitution matrix, which reflects the likelihood of amino acid substitutions. This completes the log odds score computation. After compiling all substitution probabilities of possible amino acid mutations, a 20*20 PAM matrix is established.
- 9. PAM250Amino Acid Similarity Matrix Substitution of an Aspartic acid for glutamic acid (both acidic) adds 3 to the score. Substitution of the positively charged Lys for the nonpolar Pro adds -1 to the score. Generally, the more conservative the replacement, the higher the value that will be added to the score. CONSTRUCTION OF PAM (cont.)
- 10. SCORES IN PAM MATRICES Positive scores in the matrix denotes substitutions occurring more frequently than would have occurred by random chance or expected among evolutionary conserved replacements in a dataset of homologous sequences. A zero score means that the frequency of amino acid substitutions found in homologous sequence data set is equal to that expected by chance. In this case, the relationship between the amino acids is weakly similar at best in terms of physicochemical properties. Negative score corresponds to substitutions found in homologous sequence dataset less frequent than would have occurred by random chance. This normally occurs with substitutions between dissimilar residues.
- 11. PAM MATRICES’ NUMBERS PAM-1 is a scoring system for sequence in which 1% of the residue have undergone mutation. The increasing PAM numbers correlate with increasing PAM units & thus evolutionary distances of protein sequences. (PAM-250 represents 250% mutation i.e., an average of 2.5 accepted mutation per residue-a very distant relationship.) Pam matrices with power serial numbers are more suitable for aligning more closely related sequences. Other Pam matrices with increasing numbers for more divergent sequences are extrapolated from PAM1 through matrix multiplication. For example, PAM80 is produced by values of the PAM1 matrix multiplied by itself eighty times. The mathematical transformation accounts for multiple substitutions having occurred in an amino acid position during evolution.
- 12. PAM MATRICES’ NUMBERS(cont.) If mutation is observed as F replaced by I, the evolutionary changes may have actually undergone a number of intermediate steps before becoming I, such as in the given sequence F -> M -> L -> I. So, a PAM80 matrix only corresponds to 50% of observed mutational rates. PAM tries to model what happens at long evolutionary distances based on a simple Morkov model derived from closely related sequences For PAM250, which corresponds to an to 20%amino acid identity, represents 250 mutations per 100 residues. In theory, the number of evolutionary changes approximately corresponds to an expected evolutionary span of 2,500 million years
- 13. MORE ABOUT PAM MATRICES Substitution matrices like PAM250 are constructed by observing the frequencies of amino acid replacements in large samples of protein sequences. For a given replacement, the PAM value is proportional to the natural log of the frequency with which that replacement was observed to occur. For closely related sequences, it is appropriate to use PAM 100 matrix in which PAM units have been extrapolated to 100% replacement. Most database searches use PAM 250 matrix since larger databases will tend to have sets of more distantly-related sequences.
- 14. MORE ABOUT PAM MATRICES(cont.) Nucleotide scoring matrices have been developed for scoring DNA sequence alignments, on similar lines as amino acid scoring matrices. DNA matrices can include ambiguous DNA symbols and information from mutational analysis. Typical information about mutation included is that transitions are more probable than transversions.
- 15. REFERENCES 1. Scoring matrices. Ashwini S Mushunuri.BBI-2-13010. https:// www.slideshare.net/ashwinimushunuri96/scoring-matrices. 2. Point accepted mutation. https://en.wikipedia.org/wiki/ Point_accepted_mutation 3. Adansonian Classification - Medical Definition from MediLexicon www.medilexicon.com/dictionary/18016 4. S.C. Rastogi, Namita Mendiratta, Parag.Rastogi. Bioinformatics concepts, Skills & Applications. CBS Publishers & distributors. New Delhi. http://www.cbspd.com