cdskit backalign

cdskit backalign back-aligns CDS sequences based on an amino acid alignment.

Example

In this example, CDSKIT generates a codon alignment from unaligned CDS sequences and an aligned amino acid sequence file.

Command

cdskit backalign --seq_file unaligned_cds.fasta --aa_aln aligned_aa.fasta --out_file aligned_cds.fasta

unaligned_cds.fasta

>seq1
ATGAAACCC
>seq2
ATGAAAGGG

aligned_aa.fasta

>seq1
MK-P
>seq2
MKG-

aligned_cds.fasta

>seq1
ATGAAA---CCC
>seq2
ATGAAAGGG---

Notes

• Sequence IDs in --seq_file and --aa_aln should match.
• --aa_aln should be aligned (all sequences should have the same length).
• CDS lengths in --seq_file should be multiples of three after removing gap characters.
• A terminal stop codon in CDS can be omitted in --aa_aln.

For trimmed protein alignments, use backtrim with the trimmer's retained column positions. Backalign requires the complete corresponding protein sequence (apart from the documented terminal stop exception); it cannot infer deleted codon positions from repeated amino acids.

References

Cite the method or resource actually used and report the CDSKIT version and options.

• Cock PJA et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422–1423. Paper — Sequence parsing, feature extraction and genetic-code infrastructure used by CDSKIT.