16S rRNA alignment

Question

[m.sabrysarhan]

Could you please give me some codes to align 16S rRNA sequences using clustalW on BioLinux, I'm quite new linux user. I have 50 seq. length about 1500

I want to do MSA and build a Phylogenetic tree for publication

[Ram]

Did you read the Clustal manual? What part are you facing difficulties with? And "build a tree for a publication" sounds like you're being asked to do something without being given the bigger picture. Is that the case? Can you please share your objective for the MSA+tree with us?

[m.sabrysarhan]

I have some 16S rRNA sequences for newly isolated bacteria, I'd like to precisely determine the nearest neighbour within the species level, so, I have obtained all species belongs to that genus and I'd like to align them with mine. presenting this for publication.

that is the case exactly

Answer 1

[Erik Wright]

Since this question is tagged with R, you can use the DECIPHER package to perform sequence alignments and find the nearest neighbor (as requested in the comment by m.sabrysarhan). Assuming that you are starting with sequences in a FASTA file:

library(DECIPHER)

# align the sequences
seqs <- readDNAStringSet("<<REPLACE WITH PATH TO FASTA FILE>>")
aligned <- AlignSeqs(seqs)

# find the nearest neighbors
d <- DistanceMatrix(aligned)
diag(d) <- NA # prevent trivial distances of zero
apply(d, 1, which.min) # indices of nearest neighbors

This returns a vector with the index of the nearest neighbor to each sequence. Hope that helps!

Answer 2

[Naren]

If using clustalW is not a need then try R-COFFEE

It will give alignment visualizations as well as trees.

You can also try MEGA for Windows or MAC.

or

MUSCLE is also a good option.

Answer 3

[Benn]

You can try ADOMA for nice figures for publication, it uses the clustal W algorithm but changes the output for easier interpretation.

ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output

Answer 4

[satanicodr]

The 16S rRNA molecule has secondary structure and an aligner that does not consider this is not good for phylogeny. If you want to find its closest relative just go to a specialized database such as the Ribosomal database project or the Silva database. There you will be able to find all related sequences from isolates and environmental sources and determine the novelty.