COATi: Statistical Pairwise Alignment of Protein-Coding Sequences.

ABSTRACT: Sequence alignment is an essential method in bioinformatics and the basis of many analyses, including phylogenetic inference, ancestral sequence reconstruction, and gene annotation. Sequencing artifacts and errors made during genome assembly, such as abiological frameshifts and incorrect early stop codons, can impact downstream analyses leading to erroneous conclusions in comparative and functional genomic studies. More significantly, while indels can occur both within and between codons in natural sequences, most amino-acid- and codon-based aligners assume that indels only occur between codons. This mismatch between biology and alignment algorithms produces suboptimal alignments and errors in downstream analyses. To address these issues, we present COATi, a statistical, codon-aware pairwi

SUBMITTER: Garcia Mesa JJ 

PROVIDER: S-EPMC11255384 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature