Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD-Reference-Cited by-同舟云学术

Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD

Published:2023-07-17 Issue:1 Volume:24 Page:
ISSN:1474-760X
Container-title:Genome Biology
language:en
Short-container-title:Genome Biol

Author:

Grigorjew Andreas,Gynter Artur,Dias Fernando H. C.,Buchfink Benjamin^ORCID,Drost Hajk-Georg^ORCID,Tomescu Alexandru I.

Abstract

AbstractSequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived from suboptimal solutions is ignored. We argue that one optimal alignment per pairwise sequence comparison is a reasonable approximation when dealing with very similar sequences but is insufficient when exploring the biodiversity of the protein universe at tree-of-life scale. To overcome this limitation, we introduce pairwise alignment-safety to uncover the amino acid positions robustly shared across all suboptimal solutions. We implement EMERALD, a software library for alignment-safety inference, and apply it to 400k sequences from the SwissProt database.

Funder

Max-Planck-Gesellschaft

HORIZON EUROPE European Research Council

Academy of Finland

Max Planck Institute for Biology Tübingen

Publisher

Springer Science and Business Media LLC

Link

https://link.springer.com/content/pdf/10.1186/s13059-023-03008-6.pdf

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