CNCA

CNCA aligns multiple small, closely related annotated genomes, typically viruses, using information from both protein and nucleotide sequences to guarantee no frameshifts.

Key Features:

• Genome Alignment Integration: CNCA constructs multiple alignments that integrate both coding and non-coding sequences.
• Frameshift Prevention: CNCA generates a nucleotide alignment that is updated based on protein sequence alignment, ensuring the final nucleotide alignment matches the protein alignment with no frameshifts.
• GenBank Input Compatibility: CNCA aligns annotated genomes from GenBank files.
• Size and Relatedness Constraints: CNCA is designed for closely related small genome sequences up to 50 kb for which gene order is conserved.

Scientific Applications:

• Viral Genome Alignment: CNCA constructs alignments of small annotated genomes, typically viruses, for evolutionary history analysis.
• Coding and Non-Coding Region Preservation: CNCA preserves regions traditionally ignored in conventional back-translation methods, such as non-coding regions.
• SARS-CoV-2 Proximal Origin Studies: CNCA was developed to construct alignments of genomes closely related to SARS-CoV-2 using both coding and non-coding sequences.

Methodology:

CNCA generates a nucleotide alignment that is then updated based on the protein sequence alignment to produce a final nucleotide alignment matching the protein alignment.