CNCA aligns small annotated genomes

• Published in: BMC bioinformatics Vol. 25; no. 1; pp. 89 - 4
• Main Authors: Lorenzi, Jean-Noël, Graner, François, Courtier-Orgogozo, Virginie, Achaz, Guillaume
• Format: Journal Article
• Language: English
• Published: London BioMed Central 29.02.2024; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Alignment; Amino acid sequence; Amino acids; Annotated genomes; Annotations; Authorship; Bioinformatics; Biomedical and Life Sciences; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Coronaviruses; COVID-19; Evolutionary genetics; Evolutionary Studies; Gene order; Gene sequencing; Genetic aspects; Genetic research; Genetics; Genomes; Genomics; Life Sciences; Microarrays; Nucleotide alignment; Nucleotide sequence; Nucleotides; Protein alignment; Proteins; Python; Quantitative Methods; Severe acute respiratory syndrome coronavirus 2; Software; Technology application; Viral diseases; Web applications; France; Nucleotide alignment; Annotated genomes; Protein alignment; annotated genomes; nucleotide alignment; protein alignment
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05700-1

Background To explore the evolutionary history of sequences, a sequence alignment is a first and necessary step, and its quality is crucial. In the context of the study of the proximal origins of SARS-CoV-2 coronavirus, we wanted to construct an alignment of genomes closely related to SARS-CoV-2 using both coding and non-coding sequences. To our knowledge, there is no tool that can be used to construct this type of alignment, which motivated the creation of CNCA. Results CNCA is a web tool that aligns annotated genomes from GenBank files. It generates a nucleotide alignment that is then updated based on the protein sequence alignment. The output final nucleotide alignment matches the protein alignment and guarantees no frameshift. CNCA was designed to align closely related small genome sequences up to 50 kb (typically viruses) for which the gene order is conserved. Conclusions CNCA constructs multiple alignments of small genomes by integrating both coding and non-coding sequences. This preserves regions traditionally ignored in conventional back-translation methods, such as non-coding regions.