What is PAM and BLOSUM matrix?

PAM matrices are used to score alignments between closely related protein sequences. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences.

What is PAM 250 matrix?

PAM matrices are a common family of score matrices. Thus, using the PAM 250 scoring matrix means that about 250 mutations per 100 amino acids may have happened, while with PAM 10 only 10 mutations per 100 amino acids are assumed, so that only very similar sequences will reach useful alignment scores.

What is the role of the PAM and BLOSUM tables?

The PAM and BLOSUM score matrices account for multiple substitutions in radically different ways. The PAM matrices for amino acids, along with the single letter abbreviations used for genetically encoded amino acids, were developed by Margaret Dayhoff.

Why are PAM Matrices Nonreciprocal?

The PAM matrices are considered nonreciprocal, meaning that the probability of changing an amino acid such as alanine to arginine is not equal to the probability of changing an arginine to an alanine.

What is Blosum in bioinformatics?

In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. They are based on local alignments.

How are BLOSUM matrices generated?

BLOSUM stands for BLOcks SUbstitution Matrices (Henikoff & Henikoff, 1992), and were created by observing substitution frequencies in local ungapped multiple sequence alignments. The score reflects the chance (log-odds) one amino acid is substituted for another in a set of protein multiple sequence alignments.

How is PAM matrix calculated?

The PAM matrix is usually organized by dividing the amino acids to groups of relatively similar amino acids and all group members are located in consecutive columns in the matrix.

What does positive and negative indicate in a PAM scoring matrix?

A score of zero indicates that the frequency with which a given two amino acids were found aligned in the database was as expected by chance, while a positive score indicates that the alignment was found more often than by chance, and negative score indicates that the alignment was found less often than by chance.

What is BLOcks in BLOSUM Matrix?

BLOSUM matices are calculated from blocks of highly conserved amino acid sequences with a certain degree of similarity between these sequences. Matrix constructed from no more than x\% similarity is called BLOSUM-x matrix.

What does a high BLOSUM score mean?

The interpretation is that the higher the score, the more likely the corresponding amino-acid substitution is. The wikipedia article on BLOSUM has a good explanation, check the section on scoring.