AI Article Synopsis
- Researchers created a web tool called CNCA to align genomes related to the SARS-CoV-2 coronavirus, focusing on both coding and non-coding sequences, as no existing tools met their needs.
- CNCA processes GenBank files to produce a nucleotide alignment that aligns with protein sequence alignments, ensuring consistency and no frameshift errors.
- The tool allows for proper alignment of small genome sequences, preserving important non-coding regions often overlooked in traditional methods.
Article Abstract
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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10905818 | PMC |
| http://dx.doi.org/10.1186/s12859-024-05700-1 | DOI Listing |
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