Systematic exploration of guide-tree topology effects for small protein alignments.

ABSTRACT:

Background

Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree construction schemes are based on pair-wise distances amongst unaligned sequences. Others try to emulate an underlying evolutionary tree and involve various iteration methods.

Results

We explore all possible guide-trees for a set of protein alignments of up to eight sequences. We find that pairwise distance based default guide-trees sometimes outperform evolutionary guide-trees, as measured by structure derived reference alignments. However, default guide-trees fall way

SUBMITTER: Sievers F 

PROVIDER: S-EPMC4287568 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature