extracting certain region 16sRNA from Silva

Question

[Quak]

I would like to extract V4 region from all available sequences on Silva; If I am not mistaken, Silva is a 16sRNA database, but it does not have such annotate on its 16sRNA sequences.

Answer 1

[dago]

Looking here you will see the location and structure of the V4 region

http://www.nature.com/nrmicro/journal/v12/n9/fig_tab/nrmicro3330_F1.html

Then Import Silva db in ARB, open the alignment editor and there you should be able to recover that region. At the moment my ARB is not working, so I cannot give u more details. But maybe you could give it a try and figure it out by your self the right way of doing it.

[Quak]

I believe the one you sent is only for Escherichia coli,

how about other species ?! I don't think, they would necessarily even be with the same length

[dago]

The alignment Silva and ARB are using refer to E. coli. When you submit your seqs for alignment they do not perform a de-novo alignment but align you seqs on the reference. That's why I think it would make sense to use ARB to take the reference position

[Quak]

o - cool - does that mean, I should download the aligned file; or the pure fasta file and align it against E. coli and ... ? Thanks

[dago]

I thought you could just download the silva, load it into ARB and use the alignment editor to extract what u need.

Answer 2

[Brian Bushnell]

BBMap contains tools for this purpose, based on primer sequences. Let's say you want the region between primers "ACGT" and "CCCC":

msa.sh in=16s.fa out=x.sam literal=ACGT
msa.sh in=16s.fa out=y.sam literal=CCCC
cutprimers.sh in=16s.fa out=V4.fa sam1=x.sam sam2=y.sam

If you have multiple primers, use a comma-delimited list such as literal=ACGT,ACTT.