FAQs
Archives
- I have a list of old Ensembl IDs from a previous release. How can I find their IDs in the current version?
- When is new data (eg new dbSNP build, a genome assembly, or updated ENCODE data) released on Ensembl ?
Genome assemblies
- What is a genome assembly?
- What human genome assembly and coordinate system is Ensembl using?
- What haplotypes and assembly patches can I see for human?
Compara API
- How can I obtain the constrained elements, i.e the conserved sequences, for multiple species?
- Can I get the conservation scores (GERP scores) for nucleotides in whole genome alignments?
Comparative genomics
- How do I see multi-species comparisons?
- How does Ensembl determine homology relationships?
- Can I view syntenic regions in Ensembl?
- I would like a list of homologues to my gene. Should I look at the gene trees or the families?
Core API
Export, uploads and downloads
- How do I convert IDs? I have ENSG... IDs and I would like HGNC symbols and EntrezGene IDs along with matching Affymetrix platform HC G110 probes.
- How can I export sequence?
- How can I download all the gene/transcript/protein sequences for a species? Do I use BioMart?
- I've created a customised view in Ensembl. Can I share this with my colleagues and collaborators by email?
- Is there a list of all species and corresponding metadata available in Ensembl Genomes?
- Can I install a local copy of the Ensembl database(s)?
- Can I export a nice picture of my data in Ensembl?
- I would like to export an image of a particular view in Ensembl. Which image export option should I use?
- Ensembl BioMart shows results for protein-coding genes when protein-associated attributes are chosen. Non-coding genes that pass filters will not be shown in the results if certain protein-associated attributes are chosen. Why does this occur?
Genes
- Can I view exons, introns, and flanking sequence to a transcript?
- What is the difference between Ensembl, Havana and Ensembl/Havana merged transcripts? And what does known and novel mean?
- Which transcript should I use?
- How do I access RefSeq annotation in Ensembl?
- My gene has changed, and I don't know why.
- What is GENCODE?
- How can I view RNASeq data in Ensembl?
- I've identified some new genes/transripts/RNASeq reads and would like them to be added to the Ensembl gene set. How do I submit them?
- What do the different biotypes in Ensembl mean?
Regulation
- Where can I find DNA Methylation data?
- How can I view and download gene regulation data... and where did it come from?
- How do I download the promoter sequence for my gene of interest?
Variation
- Where are disease and phenotype associations from OMIM (for human)?
- What is an LRG?
- What do the population codes for human allele frequencies mean?
- How do you define the cut-off between an indel and a structural variant?
- Does Ensembl report variation alleles on the forward strand or reverse strand?
- What does the evidence status mean for a variant?
Other data
- How do I view clone sets, such as BACs?
- Why do I see different hits when I use BLAT or BLAST from Ensembl, UCSC, and NCBI?
- What styles are available for the data tracks in views like Region in detail?
- How do I cite Ensembl?
- What are the differences between BLAST and BLAT?
- What is an Ensembl release?
- I have an Ensembl ID, what can I tell about it from the ID?
If you have any other questions about Ensembl, please do not hesitate to contact our HelpDesk. You may also like to subscribe to the developers' mailing list.