08. BLOSUM vs. PAM

As we have seen, there are two different log-odds scoring matrices available. When performing pairwise sequence alignments, you must specify the exact matrix to use - this depends on the suspected degree of identity between the query and its matches.

Let's do a quick summary of these two matrices and see how they differ.

PAM matrices summary

PAM (Accepted Point Mutations) matrices are:

  • Extrapolated using comparisons among closely related proteins based on an evolutionary model.
  • Based on data from alignments of closely related protein families.
  • Because they use the Markov model, the substitution probabilties for highly related proteins can be extrapolated to probabilties of distantly related proteins.

Some limitations of PAM matrices include the somewhat inaccuracy of the assumption model and each position being context dependent.

BLOSUM summary

  • Based on empirical observations of more distantly related protein alignments.
  • Not based on an evolutionary model - just empirically derived.
  • Sequence comparisons cover a broad range of divergences rather than just one subfamily of proteins.
  • Based on observed alignments from conserved regions of multiple sequence alignments (blocks). These blocks are from large protein databases, which give a large sampling site.

Limitations are that you are limited to a subset of conserved domains.

Take your Linux skills to the next level!

The Linux Command Line

Take your Linux skills to the next level! Try Linux & UNIX

The Linux Command Line takes you from your very first terminal keystrokes to writing full programs in Bash, the most popular Linux shell. Along the way you'll learn the timeless skills handed down by generations of gray-bearded, mouse-shunning gurus: file navigation, environment configuration, command chaining, pattern matching with regular expressions, and more.

$ Check price
39.9539.95Amazon 4.5 logo(274+ reviews)

More Linux & UNIX resources

Become a Bioinformatics Whiz!

Introduction to Bioinformatics Vol. 1

Become a Bioinformatics Whiz! Try Bioinformatics

If you're looking for a fun and easy entry point into bioinformatics algorithms, this book it just for you! Filled with graphics, and written in a light-hearted and humorous story-telling persona, Bioinformatics Algorithms guides you through the intricacies of the problems faced in biology, and the clever solutions used to solve them.

$ Check price
49.9949.99Amazon 4.5 logo(4+ reviews)

More Bioinformatics resources

Ad