FAQs
Archives
- Where are older or archive sites?
- I have a list of old Ensembl IDs from a previous release. How can I find their IDs in the current version?
Genome assemblies
- What is a genome assembly?
- My human gene is on HSCHR6_COX. What is that?
- What human genome assembly and coordinate system is Ensembl using?
- Where are the mosquito and honeybee genomes?
- What haplotypes and patches can I see for human?
Compara API
- How do I get alignments of homologous proteins? Can I get the CDS (coding sequence) alignments as well? I'm using the API.
- How can I obtain the conserved sequences calculated across multiple species, using the Compara API?
- 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?
- What are the blast and MCL options used to determine the Ensembl Compara MCL 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 proteins in the human proteome? Do I use BioMart?
- Can I install a local copy of the Ensembl database(s)?
- How do I upload my data to Ensembl?
Genes
- Can I view exons, introns, and flanking sequence to a transcript?
- What is the difference between Ensembl, Havana and 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?
Regulation
- Does Ensembl have promoters or regulatory regions?
- Where is the MeDIP data? How can I view and download gene regulation data... and where did it come from?
Variation
- What do the population codes for human allele frequencies mean?
- What is the Variant Effect Predictor?
- How do I show and/or retrieve variation data from the 1000 Genomes project?
- Where are disease and phenotype associations from OMIM (for human)?
- What is an LRG?
Other data
- How do I view clone sets, such as 129/AB2.2 BACs?
- Where is the MICER resource for mouse?
- Why do I see different hits when I use BLAT or BLAST from Ensembl, UCSC, and NCBI?
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.