Thursday, 4 September 2014

Quick Guide to the New Uniprot Web

Probably Uniprot is one of the most used and well-established services in bioinformatics worldwide. With more than 12 years, is one of the major resources of biological information and the reference catalog of protein sequence in the World. The aim of Uniprot is provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. It started in 2002 when the Swiss‐Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium.

Nowadays, the UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.

EMBL-EBI and SIB together used to produce Swiss-Prot and TrEMBL, while PIR produced the Protein Sequence Database (PIR-PSD). TrEMBL (Translated EMBL Nucleotide Sequence Data Library) was originally created because sequence data was being generated at a pace that exceeded Swiss-Prot's ability to keep up. Meanwhile, PIR maintained the PIR-PSD and related databases, including iProClass, a database of protein sequences and curated families.

Proteomes Sets?

A proteome consists of the set of proteins thought to be expressed by an organism whose genome has been completely sequenced.

Reference proteome sets?

Some proteomes have been (manually and algorithmically) selected as reference proteomes. They cover well-studied model organisms and other organisms of interest for biomedical research and phylogeny.

What are the differences between Swiss-Prot and TrEMBL?

UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.

The new Web!!!

How to search in the new Uniprot?

New Search box across the complete resource. The user can select the dataset and put the search text very quick. 

The six main datasets are UniProtKB, UniRef, UniParc, Proteomes, Supporting data, and Help pages.

How to retrieve ID and mapping your ID Lists?

Enter or upload a list of identifiers to do one of the following:

Retrieve the corresponding UniProt entries to download them or work with them on this website. Convert identifiers which are of a different type to UniProt identifiers or vice versa and download the identifier lists.

Protein Lists

The Uniprot browser allows the user to browse in Uniprot resources. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added.

A search result page is subdivided into a filter panel on the left, and the actual result table on the right, occupying the majority of the screen space. The filter panel provides different filters to the final list of proteins such as taxonomy, organism or if the proteins is reviewed or unreviewed.

The Uniprot Entry View

Major features:

* More clear, fast and simple web design.
* More documentation including videos, tutorials and course materials.
* More resources: Proteomes, Supporting Information
* Better integration between resources.
* Better usability in terms: more intuitive, well-structured and best navigation.

Well done Uniprot Team!!

No comments:

Post a Comment

Note: only a member of this blog may post a comment.