New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

Frontiers in Bioinformatics

Bioinformatics

Kejue Jia¹  Mesih Kilinc²  Robert L. Jernigan² 

[1] Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States;Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States;Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States;

关键词: protein sequences;    sequence alignment algorithm;    coevolution information;    disordered proteins;    function from sequence alignment;   

DOI  :  10.3389/fbinf.2023.1227193

 received in 2023-05-22, accepted in 2023-08-14,  发布年份 2023

来源: Frontiers

【 摘 要 】

Understanding protein sequences and how they relate to the functions of proteins is extremely important. One of the most basic operations in bioinformatics is sequence alignment and usually the first things learned from these are which positions are the most conserved and often these are critical parts of the structure, such as enzyme active site residues. In addition, the contact pairs in a protein usually correspond closely to the correlations between residue positions in the multiple sequence alignment, and these usually change in a systematic and coordinated way, if one position changes then the other member of the pair also changes to compensate. In the present work, these correlated pairs are taken as anchor points for a new type of sequence alignment. The main advantage of the method here is its combining the remote homolog detection from our method PROST with pairwise sequence substitutions in the rigorous method from Kleinjung et al. We show a few examples of some resulting sequence alignments, and how they can lead to improvements in alignments for function, even for a disordered protein.

【 授权许可】

Unknown   
Copyright © 2023 Jia, Kilinc and Jernigan.