The number of fully sequenced genomes of yeasts is dramatically increasing but both structural and functional annotation quality are usually neglected, as most frequently based on automatic annotation transfer tools from reference genomes. RNA sequencing technologies offer the possibility to better characterize yeast transcriptomes and to correct or improve the prediction of mRNA, ncRNA, or miscellaneous RNA. We describe a computational approach to enhance structural annotation of yeast genomes based on RNA-Seq data exploitation. The proposed pipeline is primarily based on read mapping with TopHat2. Mapping outputs are then used for various applications such as: (1) validation of exon-exon junctions of predicted transcripts, (2) definition of new transcribed features, (3) prediction of 3' UTR, and (4) identification of extra features absent from the genome assembly. We strongly encourage curators to proceed to a manual validation and editing of the reference genome. Releasing genomes with high-quality annotation is an important issue, as they will be considered as references for further predictions.
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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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Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.
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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