Question: RNAmmer rna prediction
1
gravatar for alebuenosm
4.0 years ago by
alebuenosm20
Brazil
alebuenosm20 wrote:

High. I used the RNAmmer site to search for rRNA genes in a draft prokaryotic genome. RNAmmer found rRNA genes, but curiously they are not in a operon. The software found three 5s genes distributed in three different contigs and another 16S rRNA in another contig. This makes no sense as there must be an operon. Have you ever seen something like this  and is there another tool that can be used to search for rRNA genes? ( tRNAs were already succesfully predicted with ARAGORN)

myposts • 1.8k views
ADD COMMENTlink modified 4.0 years ago by 5heikki8.6k • written 4.0 years ago by alebuenosm20
1
gravatar for 5heikki
4.0 years ago by
5heikki8.6k
Finland
5heikki8.6k wrote:

You can fetch relevant CMs from Rfam and use them with infernal. However, consider the assembly process. Assemblies tend to break in repetitive regions, no? Since there are multiple rRNAs in prokaryote genomes, they can be considered repetitive regions, no? IMO it's only natural that you'll find partial rRNAs from the ends of multiple contigs..

ADD COMMENTlink written 4.0 years ago by 5heikki8.6k
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: 764 users visited in the last hour