Overview
TRIFID provides pre-computed predictions and predictive features for a wide range of species and genome assemblies. Each dataset includes functionality scores for all annotated splice isoforms in the respective genome version.Pre-computed Predictions
The following table lists all available TRIFID predictions organized by genome assembly, species, and annotation source:| Genome Assembly | Species | Common Name | Model | Version | Database | Release Date | Data Access |
|---|---|---|---|---|---|---|---|
| GRCh38 | Homo sapiens | Human | Human | v1 | GENCODE | 27 - 08.2017 | Download |
| GRCh38 | Homo sapiens | Human | Human | v2 | GENCODE | 42 - 04.2022 | Download |
| GRCh38 | Homo sapiens | Human | Human | v2 | GENCODE | 37 - 02.2021 | Download |
| GRCh38 | Homo sapiens | Human | RefSeq | v2 | RefSeq - NCBI | 110 - 02.2020 | Download |
| GRCh37 | Homo sapiens | Human | RefSeq | v2 | RefSeq - NCBI | 105 - 02.2020 | Download |
| GRCh37 | Homo sapiens | Human | Human | v2 | GENCODE | 19 - 12.2013 | Download |
| GRCm39 | Mus musculus | Mouse | Mouse | v2 | GENCODE | 31 - 04.2022 | Download |
| GRCm38 | Mus musculus | Mouse | Mouse | v2 | GENCODE | 25 - 11.2019 | Download |
| mRatBN7.2 | Rattus norvegicus | Rat | Vertebrates | v2 | Ensembl | 105 - 12.2021 | Download |
| GRCz11 | Danio rerio | Zebrafish | Vertebrates | v2 | Ensembl | 104 - 05.2021 | Download |
| GRCg7b | Gallus gallus | Chicken | Vertebrates | v2 | Ensembl | 108 - 10.2022 | Download |
| Pan_tro_3.0 | Pan troglodytes | Chimpanzee | Vertebrates | v2 | Ensembl | 104 - 05.2021 | Download |
| Sscrofa11.1 | Sus scrofa | Pig | Vertebrates | v2 | Ensembl | 108 - 10.2022 | Download |
| ARS-UCD1.2 | Bos taurus | Cow | Vertebrates | v2 | Ensembl | 104 - 05.2021 | Download |
| Mmul_10 | Macaca mulatta | Macaque | Vertebrates | v2 | Ensembl | 105 - 12.2021 | Download |
| BDGP6 | Drosophila melanogaster | Fruitfly | Invertebrates | v2 | Ensembl - Flybase | 107 - 07.2022 | Download |
| WBcel235 | Caenorhabditis elegans | Worm | Invertebrates | v2 | Ensembl - Wormbase | 108 - 10.2022 | Download |
Model Versions
v1 (Initial Release)
The initial TRIFID model trained on GENCODE Release 27 (GRCh38.p10) with 45 predictive features. Released in March 2021.v2 (Current Release)
The updated TRIFID model with 47 predictive features (2 additional features added). Released in September 2022 with support for multiple species and genome assemblies.Dataset Contents
Each sharepoint contains:- Predictions file: TRIFID functionality scores for all isoforms
- Features file: All 47 predictive features used by the model
- Metadata: Gene and transcript annotations
File Format
Prediction files are provided as compressed TSV files (trifid_predictions.tsv.gz) with the following columns:
transcript_id: Ensembl transcript identifiergene_id: Ensembl gene identifiergene_name: Gene symboltrifid_score: Functionality probability (0-1)appris: APPRIS annotation label- Additional feature columns
Requesting New Data
If you need predictions for a specific genome version or species not listed above, please open an issue on the GitHub repository.Related Resources
- TRIFID Training Set (GENCODE 27)
- Tutorial Notebook
- Figures Notebook