- Course overview
- Search within this course
- Why Ensembl?
- What is Ensembl?
- When to use Ensembl
- How to access Ensembl
- How to search Ensembl
- Exploring sources of biological data
- Navigating Ensembl
- Customise Ensembl
- Manage your data
- Export data
- Download data with BioMart
- Bulk download genome-wide data files with FTP
- Ensembl tools
- Summary
- Guided examples of using Ensembl
- Exercises
- Your feedback
- Get help and support on Ensembl
- Acknowledgements
- Learn more
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Ensembl tools
Click the tools button at the top of the browser to reveal some useful programs (Figure 47).
Each tool has an online interface and an API script to be used in conjunction with the Ensembl Perl API.
The Variant Effect Predictor is our most popular tool. Enter in transcript or genomic coordinates to determine the effect of sequence variation on transcripts and proteins. A dbSNP identifier will be given in the output, if there is a matching one.
The Assembly Converter allows coordinates from an older genome sequence to be updated to new coordinates (and vice-versa). As genomes are sequenced, the improved technology allows current genome sequence to be more accurate, containing fewer gaps and fewer mistakes. Using the most recent genome version or assembly is advised.
ID History converter displays IDs that are in the current version of Ensembl. Start with a list of old IDs, and see which ones are still used, and which ones have been ‘retired’, or changed into a different ID. Though Ensembl IDs are stable (a gene or transcript should always have the same ID), the ID can change if one gene is split into two, or two genes that were erroneously split in a previous release are fused together into one.
File Chameleon allows customised download of genome-wide files for use with NGS analysis tools.
VCF to PED converter parses a VCF file to create a linkage pedigree file (PED) and a marker information file, which together may be loaded into other variation data analysis tools, such as PLINK and Haploview. You can choose to convert a VCF file of data taken from the 1000 Genomes project, or you can supply the VCF to PED Converter tool with your own files.
Data Slicer provides an interface which allows users to get subsections of either VCF (VCFtools) or BAM (SAMtools) files based on genomic coordinates. This tool is currently available for GRCh37 only.
Linkage Disequilibrium Calculator (LD) calculator is a tool for calculating LD between variants using genotypes from a selected population.
 Archive sites let you view past versions of Ensembl, including older gene sets. |