Question: 16S-specific multiple alignment of rDNA sequences
0
gravatar for predeus
5 weeks ago by
predeus1.3k
Russia
predeus1.3k wrote:

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.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by predeus1.3k

Thank you for all suggestions - extremely useful!

ADD REPLYlink written 5 weeks ago by predeus1.3k
2
gravatar for Mensur Dlakic
5 weeks ago by
Mensur Dlakic5.4k
USA
Mensur Dlakic5.4k wrote:

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.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Mensur Dlakic5.4k
2
gravatar for lakhujanivijay
5 weeks ago by
lakhujanivijay5.0k
India
lakhujanivijay5.0k wrote:

Di you try PyNAST ? PyNAST is pythonic implementation of NAST

ADD COMMENTlink written 5 weeks ago by lakhujanivijay5.0k
1
gravatar for h.mon
5 weeks ago by
h.mon29k
Brazil
h.mon29k wrote:

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

ADD COMMENTlink written 5 weeks ago by h.mon29k
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