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Contents

1. About RBPDB
2. Browsing
3. Searching
4. Downloading data
5. Scanning sequences

1. About RBPDB

RBPDB is a collection of RNA-binding proteins linked to a curated database of published observations of RNA binding. For a description of the database, including types of proteins and experiments represented, data sources, and curation methodology, please refer to the RBPDB paper at Nucleic Acids Research.

2. Browsing

Data in RBPDB is separated into two sets: proteins and experiments. Each experiment is an observation of RNA-protein binding to a single sequence (e.g. in a gel shift or UC cross-linking experiment) or many sequences (e.g. a SELEX or RIP-chip experiment). Each experiment is linked to a single RNA-binding protein.

The full data set can be browsed by proteins or experiments by clicking the link on the top of the page. To view more information on a protein or experiment, click view. From the proteins page, you can also access a list of experiments associated with that protein or INPARANOID [1] orthologs of that protein.

3. Searching

RBPDB can be searched in a variety of different ways. Proteins can be quickly searched by gene symbol, name or description, and experiments by experiment type, sequence or PubMed ID through the search boxes at the top of every page.

Through the advanced search page, more complex queries can be constructed to retrieve proteins by species or RNA-binding domain. Similarly, experiments can be searched by all the protein search options (which will retrieve experiments on proteins matching those specifications) as well as by experiment type, and whether the experiment has a Position Weight Matrix (PWM) associated with it.

Finally, the tables of proteins and experiments can be filtered further by clicking the "Filter" button above the table.

4. Downloading data

Proteins and experiments from browsing or returned by search results can be exported in a variety of formatsby clicking the buttons below the table. The formats are: plain text (denoted by a notebook icon: ), CSV (), html (), excel (), and word ().

As well, bulk download files of experiments, proteins, matrices and sequences from in vivo immunoprecipitation experiments can be downloaded from the Downloads page. Read the README file associated with these files for more information.

5. Scanning sequences

DNA or RNA sequences can be scanned with the set of PWMs in the database through a form on the homepage. The sequence scan scores every possible site in the submitted sequence, and returns every site that scores at least 80% of the maximum possible score for that matrix. The scan is sensitive but not very selective.

6. References

1. Berglund AC, Sjolund E, Ostlund G, Sonnhammer ELL "InParanoid 6: eukaryotic ortholog clusters with inparalogs" Nucleic Acids Res. 36:D263-266 (2008).