Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.

ABSTRACT: Low complexity regions are fragments of protein sequences composed of only a few types of amino acids. These regions frequently occur in proteins and can play an important role in their functions. However, scientists are mainly focused on regions characterized by high diversity of amino acid composition. Similarity between regions of protein sequences frequently reflect functional similarity between them. In this article, we discuss strengths and weaknesses of the similarity analysis of low complexity regions using BLAST, HHblits and CD-HIT. These methods are considered to be the gold standard in protein similarity analysis and were designed for comparison of high complexity regions. However, we lack specialized methods that could be used to compare the similarity of low complexity regions

SUBMITTER: Jarnot P 

PROVIDER: S-EPMC9487646 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature