A benchmark study of sequence alignment methods for protein clustering.

ABSTRACT:

Background

Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleotide sequence alignments. To test whether similar drawbacks also influence protein sequence alignment analyses, we propose a new benchmark framework for protein clustering based on cluster validity. This new framework directly reflects the biological ground truth of the application scenarios that adopt sequence alignments, and evaluates the alignment quality according to the achievement of the biological goal, rather than the comparison on sequence level only, which a

SUBMITTER: Wang Y 

PROVIDER: S-EPMC6311937 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature