Hi Valentina,

I think one of the most common tools for predicting genes (introns and exons) in fungi is Augustus. The tool is not demanding, so you can run it locally without many resources, or you can also use their web server for it:

https://bioinf.uni-greifswald.de/augustus/submission.php

The most common use is to do gene prediction on the whole genome, but if you provide your region of interest or your gene sequence, it will also predict it.

You will need to choose a suitable fungal model from the list. If you choose the closest species to yours, it should be fine (there are a few basidiomycete models). Bear in mind that the prediction is based on other species. That means that if you do not have mRNA seq data to base your prediction, the prediction might not be 100% accurate (there might be some fewer or extra amino acids around the introns), but it's usually good for functional annotation. For structure prediction, I never tested. If you have any references, might be worth doing an alignment, just in case.

Good luck!

Marco

For removing introns and extracting exons from your nucleotide sequence, web-based gene prediction tools are the best option since they don’t require heavy installation or strong computer power. Among the most widely used is AUGUSTUS, which allows you to paste your sequence into a web server and obtain predicted exon–intron structures. It supports several fungi, including some Basidiomycetes, making it a practical starting point. Another simple option is GENSCAN, though it was originally trained on vertebrate data and may be less accurate for fungi.

For fungal-specific predictions, NetAspGene is a good alternative because it was designed to recognize intron–exon boundaries in fungi such as Aspergillus and related groups. While Basidiomycetes are not identical, this tool still performs better than purely vertebrate-trained predictors. Additionally, WebScipio can be very useful if you have access to a related protein sequence, since it maps that protein back to your DNA to reconstruct the exon–intron structure, often improving accuracy when working with less-studied genomes.

In your case, with a Basidiomycete sequence and limited computational resources, I recommend starting with the AUGUSTUS web server, trying the closest fungal model available. Next, run the same sequence through NetAspGene for comparison. If you can find a homologous protein from a related Basidiomycete, use WebScipio to refine the gene model. The exons predicted by these tools can then be concatenated into a coding sequence, translated into amino acids, and used directly for protein structure prediction with AlphaFold.

Here are direct links to the three web servers:

AUGUSTUS (WebAUGUSTUS) – Bioinformatics Group, Universität Greifswald

https://bioinf.uni-greifswald.de/augustus/

NetAspGene 1.0 – DTU Health Tech (for fungal splice site / exon-intron prediction)

https://services.healthtech.dtu.dk/services/NetAspGene-1.0/

WebScipio – Converts a protein query + genome assembly into predicted gene/exon-intron structure

http://www.webscipio.org/

You can get mRNAs from Genbank.

https://www.ncbi.nlm.nih.gov/search/all/?term=Basidiomycetes

Download the mRNA sequences directly from their database.