Hi, i have a question about the identification of 16S rRNA gene. One of the common methods is to resequence the 16S rRNA gene and the other is to search the database, such as greengenes. However, if i only have the genome sequence of a bacterial strain and i don't want to resequence the gene, how could i identify the 16S rRNA gene sequence of this strain quickly?
There is a long history of identifying "common" non-coding RNAs (tRNA and rRNA) and it can be done very reliably from sequence. In addition to the two excellent suggestions above (RNAmmer and Barrnap), you may want to try SSU-align:
This program will not only score small-subunit rRNAs from all three kingdoms, but it will also align them.