Collect ITS sequences from bacterial genomes

Question

[star715]

Hi, I want to build a phylogenetic tree with ITS sequences of assembled genomes. For this, I need to retrieve only ITS (internal transcribed region) sequences from a genome. Genome annotations provides annotations of rRNA sequences but not ITS. Is there any tool for that?

Currently, I can only think of blasting the genome against ITS sequences and recovering blast hits as ITS sequences from the genomes. Is there a more systematic or better approach or tool for doing it?

Thank you

[h.mon]

ITS is the region between adjacent 16S and 23S rRNA genes. As you have the 16S and 23S annotations, you can get the ITS intervals with some mathematics, and then use bedops / bedtools / samtools faidx to recover the fasta sequences of these regions.

[Mensur Dlakic]

These may be useful:

• https://ncbiinsights.ncbi.nlm.nih.gov/2020/02/21/rrna-databases/
• https://rrndb.umms.med.umich.edu/