The importance of ncRNAs in biological processes makes their annotation an essential component of any genome-sequencing project. The identification of ncRNAs in genomes requires specific expertise and tools that are distinct from the traditional protein gene annotation tools. Here, we describe the assembly of two automatic annotation pipelines, integrating publicly available tools, for homology and de novo ncRNA search in genomes. We applied both pipelines to 10 Saccharomycotina genomes and were able to find and annotate 693 ncRNA genes, corresponding to 81% of the ncRNAs expected for those genomes assuming the number of ncRNAs in Saccharomyces cerevisiae (86) as a reference. Several new ncRNAs, not yet known in the Saccharomycotina clade, were also detected. The results show the feasibility of automatic search for ncRNAs in full genomes and the utility of such approaches in large multi-genome sequencing and annotation projects.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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| Evidence ID | Analyze ID | File | Description |
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