CSC8312 -- Bioinformatics Theory and Applications

Uniprot

ENSEMBL contains information which has been generated by analysing the genome of the organism in question. This sort of knowledge is essential; the number of genomes that are available now is to great to analysis in anything other than an automatic way.

However, there are occasions when a more definitive source would be good. It is into this category that Uniprot falls. Much of knowledge in Uniprot is curated — the annotation and knowledge is organised by bioinformaticians using computational tools but adding their own expertise.

Move back to the Human ENSEMBL if you are not already there. In the "Description" section of the gene view, you should see a reference to a Uniprot record like this. Click on this. You should now be here.

Uniprot refers to several databases in one. What are the different sections called? What are the differences between them?

Features of Uniprot

Uniprot also have a RESTful interface.

Go to the location and add .txt to the URL.

You will now see the raw Uniprot record which looks like this. Like EMBL, it has the familiar two letter prefix format. Unlike with ENSEMBL, multiple transcripts are reported as variants.

The knowledge in this report varies from highly organised and structured (look at the FT lines!) to the free text (the CC lines).

Can you find a complete specification of this format? What other formats can you retrieve from Uniprot, using the REST interface?