- 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 ?
- 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?
- 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?
- 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?
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?
- Can modENCODE data be added for Drosophila species?
- 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?
- 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?
- 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?
- 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?