SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment.

ABSTRACT: Understanding how proteins mutate is critical to solving a host of biological problems. Mutations occur when an amino acid is substituted for another in a protein sequence. The set of likelihoods for amino acid substitutions is stored in a matrix and input to alignment algorithms. The quality of the resulting alignment is used to assess the similarity of two or more sequences and can vary according to assumptions modeled by the substitution matrix. Substitution strategies with minor parameter variations are often grouped together in families. For example, the BLOSUM and PAM matrix families are commonly used because they provide a standard, predefined way of modeling substitutions. However, researchers often do not know if a given matrix family or any individual matrix within a family is th

SUBMITTER: Barlowe S 

PROVIDER: S-EPMC5490468 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature