PanPA: generation and alignment of panproteome graphs.

ABSTRACT:

Motivation

Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space are still challenging due to this high diversity. In contrast, amino acid sequences have higher similarity due to evolutionary constraints, whereby a single amino acid may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, panproteomes present an attractive alternative leveraging the higher sequence similarity while not losing much of the genome in non-coding regions.

Results

SUBMITTER: Dabbaghie F 

PROVIDER: S-EPMC10748787 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature