InterProScan

Stages

1. 1.
   homology search against fungal-specific databases(broad_screen)

   The abstract explicitly states that the workflow integrates homology searches against fungal-specific databases, addressing limitations of broadly taxonomic tools for fungal transcriptomes.

   Selection: sequence homology against fungal-specific databases

2. 2.
   expression pattern-based annotation integration(secondary_characterization)

   The abstract states that expression pattern-based annotations were integrated with homology searches to highlight utility for target identification.

   Selection: expression pattern-based annotation signals integrated with homology results

3. 3.
   functional enrichment analysis(functional_characterization)

   The abstract reports that functional enrichment analyses revealed higher-resolution functional detection than existing annotation tools.

   Selection: functional enrichment of annotated transcript sets

Stages

1. 1.
   Genome re-assembly and curation(library_build)

   This stage creates the draft genome assembly that all downstream annotation steps depend on.

   Selection: Use previously generated Illumina whole-genome shotgun reads together with the corresponding GenBank assembly to produce a curated draft assembly.

2. 2.
   Ab initio gene prediction and integration(functional_characterization)

   This stage generates the structural gene annotation needed before functional annotation can be assigned.

   Selection: Predict genes with AUGUSTUS and GeneMark-ES and integrate predictions with EVidenceModeler.

3. 3.
   Functional annotation(secondary_characterization)

   This stage adds biological interpretation and external evidence support to predicted genes and proteins.

   Selection: Assign curated functions, domains, and Gene Ontology terms using eggNOG-mapper, InterProScan, and BLASTp against UniProtKB/Swiss-Prot.

4. 4.
   Completeness assessment(confirmatory_validation)

   This stage evaluates the completeness of the produced genome resource.

   Selection: Assess assembly gene space and predicted proteome completeness with BUSCO.

Steps

1. 1.
   Re-assemble and curate the argan nuclear genome draft from existing Illumina reads and the corresponding GenBank assembly

   Generate the draft assembly that serves as the substrate for downstream annotation.

   Structural and functional annotation require a genome assembly first.

2. 2.
   Run ab initio gene prediction with AUGUSTUS and GeneMark-ESgene prediction components

   Generate candidate gene models from the curated assembly.

   Gene models must be predicted before they can be integrated and functionally annotated.

3. 3.
   Integrate ab initio predictions with EVidenceModelerprediction integrator

   Combine multiple prediction outputs into a unified structural annotation set.

   Integration follows prediction because EVidenceModeler uses the upstream predictor outputs.

4. 4.
   Assign functions, domains, and Gene Ontology terms using eggNOG-mapper, InterProScan, and BLASTp against UniProtKB/Swiss-Protfunctional annotation components

   Add biological interpretation and external evidence support to predicted genes and proteins.

   Functional annotation depends on having predicted genes and proteins from the structural annotation stage.

5. 5.
   Assess assembly gene space and predicted proteome completeness with BUSCOevaluation component

   Evaluate completeness of the resulting genome resource.

   Completeness assessment is performed after assembly and annotation outputs are available.