Question: 16S rRNA alignment
0
gravatar for m.sabrysarhan
3.4 years ago by
m.sabrysarhan0 wrote:

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

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

alignment sequence R • 3.3k views
ADD COMMENTlink modified 3.3 years ago by satanicodr120 • written 3.4 years ago by m.sabrysarhan0

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?

ADD REPLYlink written 3.4 years ago by RamRS21k

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   

ADD REPLYlink written 3.4 years ago by m.sabrysarhan0
2
gravatar for Erik Wright
3.3 years ago by
Erik Wright360
Erik Wright360 wrote:

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!

ADD COMMENTlink modified 2.1 years ago • written 3.3 years ago by Erik Wright360
1
gravatar for Nari
3.4 years ago by
Nari870
United States
Nari870 wrote:

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.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Nari870
0
gravatar for Benn
3.3 years ago by
Benn6.8k
Netherlands
Benn6.8k wrote:

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

ADD COMMENTlink written 3.3 years ago by Benn6.8k
0
gravatar for satanicodr
3.3 years ago by
satanicodr120
satanicodr120 wrote:

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.

ADD COMMENTlink written 3.3 years ago by satanicodr120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 611 users visited in the last hour