16S-specific multiple alignment of rDNA sequences

Question

[predeus]

Hello all,

This is a strange question perhaps, but it's brought on by a reviewer to one of my papers. We have used mafft to generate multiple sequence alignment for a simple phylogenetic analysis. However, the reviewer suggested we use "method that takes secondary structure of 16S" into account. I take it they meant something like prank aligner that uses codon information to generate a more accurate multiple sequence alignment. However, I don't know of any such tool for 16S.

Can you recommend anything relevant? Would be grateful for any suggestions.

[predeus]

Thank you for all suggestions - extremely useful!

Answer 1

[Mensur Dlakic]

Opinions differ about this, but MAFFT - or any "regular" sequence alignment program - is generally not able to align 16S sequences properly unless they are from fairly related species. It is not a matter of codon alignment - something that understands sequence co-variation is needed to align 16S sequences properly.

SSU-ALIGN can search for 16S sequences and automatically align them based on their phylogenetic membership.

Answer 2

[h.mon]

MAFFT itself can take RNA secondary structure into account, see Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. The MAFFT online manual states the improvement in relation to regular alignment method is small, for 16S rRNA:

For relatively conserved RNAs, such as SSU and LSU rRNA, the advantage of these methods is small.

And the following page has benchmarks comparing several structural and sequence alignment methods:

https://mafft.cbrc.jp/alignment/software/eval/rna.html

Answer 3

[lakhujanivijay]

Di you try PyNAST ? PyNAST is pythonic implementation of NAST