- 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?
- 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?
- 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?
- 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?
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?
- 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?
- 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?
- 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?
- 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?