Protein embedding based alignment.

ABSTRACT:

Purpose

Despite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20-35% pairwise identity (so called "twilight zone") remains a difficult problem. Many alignment algorithms have been using substitution matrices since their creation in the 1970's to generate alignments, however, these matrices do not work well to score alignments within the twilight zone. We developed Protein Embedding based Alignments, or PEbA, to better align sequences with low pairwise identity. Similar to the traditional Smith-Waterman algorithm, PEbA uses a dynamic programming algorithm but the matching score of amino acids is based on the similarity of their embeddings from a protein language model.

Methods

We tested PEbA on over twelve thousand benchmar

SUBMITTER: Iovino BG 

PROVIDER: S-EPMC10900708 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature