02 - UniProt

Table of Contents

1. Introduction
2. The UniProt website
   1. Using UniProtKB
   2. Advanced Searches in UniProtKB
3. Exercise 01

Introduction

UniProt provides three key databases:

• The UniProt Knowledgebase (UniProtKB)
• The UniProt Reference Clusters (UniRef)
• The UniProt Archive (UniParc)

UniProtKB is likely to be the database you use most frequently to find information on gene product/protein molecular function. It is the central hub of functional information on proteins, and collates functional annotations from many other databases, ontologies, and references. It keeps records of how annotations are derived (e.g. experimentally or computationally), and is divided into two sections: one contains manually-annotated records (UniProtKB/Swiss-Prot), and a second contains computational annotations that are waiting for manual curation (UniProtKB/TrEMBL).

UniRef provides clustered sets of sequences from UniProtKB and UniParc. A number of clusterings at different stringencies are provided.

UniParc is a comprehensive, non-redundant database that contains most of the publicly-available protein sequences from a range of sources.

These databases can be queried in a number of ways, including:

• At the UniProt website http://www.uniprot.org/ in your web browser
• Sending requests to the UniProt website, using a programming language

Resources

• UniProt
• EMBL-EBI
• SIB
• PIR

The UniProt website

• Open your browser and navigate to the UniProt webpage.

The landing page offers options for each of the three main databases: UniProtKB, UniRef, and UniParc. It also offers sets of complete proteomes for a range of organisms, and databases of proteins organised by supporting data, such as literature, taxonomic classification, and subcellular location.

Using UniProtKB

• Click on the UniProtKB link. This will take you to the UniProtKB front page, with a summary of entries, and a number of links.

• Enter the word Kitasatospora in the search bar at the top of the page, and click on the Search button.

Filtering Results

• On the left of the page there's an option to filter "kitasatospora" as an organism or by taxonomy. Click on the organism filter.

• At the top left of the page there's an option to filter only the manually reviewed entries. Click on this filter.

Inspecting an Entry

• Click on the link/accession for the topmost entry.

• At the top of the page, there's a button marked History. Click on this button. A small window will open, with a link to Previous versions. Click on this link.

• Click on the Compare button.

• Compare some previous records to the current record (e.g. this comparison).

Advanced Searches in UniProtKB

In this section, you'll use the advanced searches to identify candidate human proteins that are found in the nucleus, and have been associated with some disease activity or function.

• Click on the UniProt logo to return to the landing page
• Click on the "Advanced" drop-down to get the advanced searching interface

• In the first field, select Organism [OS] with search term "Human". The dropdown will offer you several options as you type, but do not select them (you could have entered the organism "Homo sapiens" here, also).
• In the next field, keep AND on the left, and select Subcellular location with search term "nucleus". The dropdown will offer several options but, again, do not select them. At this point, allow any assertion method for the evidence code.

• Click on the plus sign (+) to get another search term field.
• In the new field, keep AND on the left, and select Pathology & Biotech with class "Disease", and no search term. At this point, allow any assertion method for the evidence code.

• Click on the magnifying glass to run the search.

Refine the search

• Click on the "Advanced" drop down. You should see that the current search populates this dialogue box.
• Change the Evidence option for the Pathology & Biotech part of the search to manual "Experimental" evidence.

• Click on the "Advanced" drop down. You should see that the current search populates this dialogue box.
• Change the Term option for the Pathology & Biotech part of the search to "melanoma".

Downloading UniProtKB Search Results

After the search above, you should be left with a small set of proteins that satisfy the following criteria:

• They derive from Homo sapiens
• They are annotated as being found in the nucleus (for which we allow any form of evidence)
• They are associated with a disease process: melanoma, and there is manually-curated experimental evidence for this association

• You can download all your search results, or just those selected with checkboxes
• Results can be downloaded compressed (gzipped) or as raw records
• Results can be downloaded as:
  • sequence data (FASTA)
  • tabular form (Excel, tab-separated)
  • computer-readable (XML, RDF)

• Download the search results as tab-separated, text, and FASTA format files
• Inspect the contents of these files

Exercise 01 (15min)

Using the UniProtKB search tools, can you find and download sets of proteins that satisfy the following requirements: