Eucaryotic gene predictor within eucaryote genome

Question

[Chvatil]

Hello everyone, I created this post to ask you some advice to find a suitable tool.

Indeed, I am looking for a program that can predict eukaryotic genes in an assembled genome. I know Augustus3.3 for example but I can't find a statistical confidence metric related to the predicted genes.

So I'm wondering if you have any advice on how to select the best tool for this:

In my case, I have genomes, I want to be sure that the predicted genes are of eukaryotic origin and not bacterial or viral for example.

Thank you

Answer 1

[Mehmet]

For gene prediction:

Augustus can be used for initial gene prediction and results can be checked at Artemis and manually curated genes can be obtained. Later, those genes can be used as reference set and the initial gene prediction results can be compared by Eval tool to get gene prediction statistics (sensitivity, specificity etc.).

For homology based: Braker2 can be used with a homology gene set composed of closely related species genes. This approach could give more insights.

For the origin:

If the species of interest interacts with some other organisms (bacteria or fungi), it is highly possible some genes may have been horizontally transferred to the the species of interest. For this some tools (darkhorse, alien index etc.) can be used to identify those genes along with phylogenetic tree analysis.

Answer 2

[Juke34]

You can find a comprehensive list of annotation tools here: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools.md.
Very few tools give confidence score to the predictions, MAKER is one the rare one. Otherwise you can use MAKER to add the confidence score over any annotation.