Identification of Internal Transcribed Spacers (ITS) in non-fungal eukaryotes

[jmartin]

Is there any software that can identify the ITS regions within a denovo assembly of a nematode species? Or do I pretty much just have to manually annotate the 18s, 5.8s & 28s and pick out regions by hand?

Assuming I am relegated to doing it by hand, can I consider everything between 18s & 5.8s as ITS1, and everything between 5.8s & 28s as ITS2? Also I'm concerned about whether I can safely use my assembly, which is from a pool of worms, or whether I need to identify single reads that span the regions to avoid having the polymorphism introduced by collapsing pooled worms down into a single assembly. Any advice would be appreciated.

[lac302]

You could create a local blast database of your denovo assembly and query with known ITS sequence looking for contigs with homology.

Also, is the pool of nematodes derived from a single genetic isolate?