The Genome Tolerance Browser is an online genome browser for visualizing the predicted tolerance of the human genome.
For each position across the genome, we compiled normalized functional predictions from numerous non-synonymous computational predictions algorithms, such as SIFT and PolyPhen,
genome-wide computational prediction algortihms, such as FATHMM-MKL and CADD,
and cancer-specific prediction algorithms, such as FATHMM-Cancer and TransFIC.
The interactive browser can be used to facilitate the rapid identification of predicted intolerant regions across the genome and can also be used to visualize the concordance & subtle differences
between multiple prediction algorithms.
If you have found this resource useful, please cite our publication:
| id | Method/Description | Download |
|---|---|---|
Non-Synonymous/Coding Prediction Algorithms |
||
| SIFT | SIFT | bigWig, bed |
| PPH2_HVAR | PolyPhen-2 (HumVar) | bigWig, bed |
| PPH2_HDIV | PolyPhen-2 (HumDiv) | bigWig, bed |
| FATHMM_MKLC | FATHMM-MKL (Coding) | bigWig, bed |
| FATHMM_U | FATHMM (Unweighted) | bigWig, bed |
| FATHMM_W | FATHMM (Weighted) | bigWig, bed |
| MA | Mutation Assessor | bigWig, bed |
| MT | MutationTaster | bigWig, bed |
| VEST | VEST | bigWig, bed |
| PROVEAN | PROVEAN | bigWig, bed |
| LRT | LRT | bigWig, bed |
| MetaLR | MetaLR | bigWig, bed |
| MetaSVM | MetaSVM | bigWig, bed |
Genome-Wide Prediction Algorithms |
||
| FATHMM_MKLNC | FATHMM-MKL (Non-Coding) | bigWig, bed |
| CADD | CADD | bigWig, bed |
| DANN | DANN | bigWig, bed |
| PP46 | PhyloP: based on the MSA of 45 vertebrate genomes to the human genome | bigWig, bed |
| PP100 | PhyloP: based on the MSA of 99 vertebrate genomes to the human genome | bigWig, bed |
| PC46 | PhastCons: based on the MSA of 45 vertebrate genomes to the human genome | bigWig, bed |
| PC100 | PhastCons: based on the MSA of 99 vertebrate genomes to the human genome | bigWig, bed |
| GERP_RS | GERP++ Rejected Substitutions (RS Scores) | bigWig, bed |
| GERP_CE | GERP++ Constrained Elements | bigWig, bed |
Cancer-Specific Prediction Algorithms |
||
| FATHMM_C | FATHMM-Cancer | bigWig, bed |
| TFIC_SIFT | TransFIC (SIFT) | bigWig, bed |
| TFIC_PPH2 | TransFIC (PolyPhen-2) | bigWig, bed |
| TFIC_MA | TransFIC (MutationAssessor) | bigWig, bed |
You can add additional tracks representing a range of computational prediction algorithms (please see the above list) using the icon. You can also add custom tracks, representing your own annotation data in bigWig and bigBed format, through the same option. Once added to the browser, the appearance of tracks (e.g. color, height etc.) can be amended using the icon.
Once you are happy with the tracks displayed in the browser, publication quality images in SVG or PNG format can be generated using the icon.
Scores used in the GTB are made available in bed format from the above
table (see Available Methods). From here, users can extract
scores pertaining to specific regions using tabix (see https://github.com/samtools/tabix).
The following syntax should be used to extract data from specific databases:
tabix <database> <chrom>:<start>-<stop>
For example, to extract SIFT GTB scores falling within 27,180,538 and 27,183,448 in chromosome 7, you
should run the following command:
tabix SIFT.bed.gz 7:27180538-27183448
The Genome Tolerance Browser is a client-side JavaScript application. This means that all rendering is performed on your web browser and not on our server. As a result, your browser may become slow or unresponsive when viewing large amounts of data. Therefore, we recommend that users remove all genome-wide prediction algorithms before zooming out too far or when searching for large genes.
We welcome any comments or suggestions that you may have regarding our browser - please send an email directly to:
We also encourage developers of functional prediction algorithms wishing to include their algorithm in our browser to contact us.