Question: RNAmmer rna prediction
gravatar for alebuenosm
4.0 years ago by
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)

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ADD COMMENTlink modified 4.0 years ago by 5heikki8.6k • written 4.0 years ago by alebuenosm20
gravatar for 5heikki
4.0 years ago by
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
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