PFASUM: a substitution matrix from Pfam structural alignments.

ABSTRACT:

Background

Detecting homologous protein sequences and computing multiple sequence alignments (MSA) are fundamental tasks in molecular bioinformatics. These tasks usually require a substitution matrix for modeling evolutionary substitution events derived from a set of aligned sequences. Over the last years, the known sequence space increased drastically and several publications demonstrated that this can lead to significantly better performing matrices. Interestingly, matrices based on dated sequence datasets are still the de facto standard for both tasks even though their data basis may limit their capabilities. We address these aspects by presenting a new substitution matrix series called PFASUM. These matrices are derived from Pfam seed MSAs using a novel algorithm and thus build

SUBMITTER: Keul F 

PROVIDER: S-EPMC5460430 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature