The Ensembl genome browser at www.ensembl.org allows scientists to investigate biological annotation of chordate (mostly vertebrate) genomes. Protein-coding and non-coding genes, splice variants, conserved regions across species, sequence variation and information about gene regulation are all available.
EnsemblGenomes at www.ensemblgenomes.org extends genome browsing to bacteria, metazoa, protists, plants and fungi.
BioMart allows all users to quickly export data in formats that can be opening in MS Excel. A Perl API allows direct access to Ensembl databases.
All Ensembl resources are free and open source. We make these videos using Camtasia (TechSmith).
Hello I have a bioinformatics related question. It's about the transcript/splice variants of the human SRSF2 gene. I searched on Ensembl to gain further insights about the topic but I find it a bit frustrating. How many exons does this gene have and how is it possible that a section of a sequence is marked as an intron in one variant but marked as a UTR in another variant? I would appreciate if you could help me find an answer to my question. Thank you.
HELP HI I have a question. I have a small list of kegg ids that I obtained from KOBAS now I want to change them to gene names using biomart but biomart is giving no output. ids look like this bna03010 (organism is brassica napus) so can you help me find a solution please?
It's now a decade since this video was put up! But if anyone still watching, can you advise? I followed the steps as per the video; but when I submitted the sequence I had in mind, to convert from hg18 to hg38, I got a little white-on-green "Done", and followed by (Download results). Looked very promising! So I did that. But instead of seeing results, I got a .bed file downloaded, which my computer couldn't open. Help!
If my data has Probe Ids alongwith Ensembl Id should I remove the probe Ids before using biomaRt package in R. Also, Ensembl Id has a suffix too, is there a need to remove them as well?
Thank you for the video! I imagine I'm too late with this question - but I was wondering if there's a way to get the transcription/pre-mRNA sequence directly from ensemble? TIA
Biomart is not too helpful in one of my studies. The bioinformatic core provided me with gene names in different formats from my proteomic data; when I tried BioMart, it was only able to show 2 or 3 updated gene names out of 70 total. Do you have any suggestions on tools that allow conversion into uniformed format from multiple resources of naming system?
Very helpful. Typically we use updated gene ID or ensembl ID for pathway analysis from proteomic or genomic analyses. I am wondering if you know any analysis tools will group genes/proteins from different species, e.g., human and viruses, to show the interactions in one specific study.
