Hello all,
I was wondering what ways are there to annotate the multiple rRNA alignments with the relative position on 16S (or 18S) consensus. To put it simply, I’d like to know for each sequence where are the approximate V1 borders, and so on.
Is there a good way to do it in Jalview?
Thank you in advance!
– Alexander
Hi Alexander
I was wondering what ways are there to annotate the multiple rRNA alignments with the relative position on 16S (or 18S) consensus. To put it simply, I’d like to know for each sequence where are the approximate V1 borders, and so on.
Is there a good way to do it in Jalview?
Just coming back to this again - You could try running RNAmmer on your alignments and importing the GFF file it produces as output:
http://www.cbs.dtu.dk/services/RNAmmer/
Jalview will highlight each hit with an ‘rRNA’ feature.
Beyond this, most genome annotation pipelines include some way of producing rRNA annotation - RNAmmer is widely used, but others also exist - such as Metaxa2 (http://microbiology.se/software/metaxa2/) - but Metaxa2 doesn’t generate results in a standard format.
Hope this helps.
Jim
On 20/07/2017 22:00, Alexander Predeus wrote: