EBI Databases Proteomics PRIDE Database-on-Demand

Database on Demand

Database on Demand is a web-based database pre-processing tool that will generate custom FASTA formatted sequence databases according to a set of user-selectable criteria using the commonly used UniProt/SWISS-PROT and UniProt/TrEMBL databases as source. New: Now includes IPI resources (note that not all filters are available for IPI).

The source is freely available under the Apache licence 2.0 from its Google code page. For feedback and questions please send an email to pride-dod@ebi.ac.uk.

NOTE: You can use the following regular expressions with the MASCOT search engine to retrieve the accession number and description from the FASTA headers in the result database. For the accession number use ">[^|]*|\([^|]*\)|" and for the description use ">[^|]*|[^|]*|\(.*\)"

Database on Demand uses the DBToolkit software (PubMedID 16030071) for its processing back-end. The development of Database on Demand
was supported by the BBSRC Tools and Resources Grant: BB/F016255/1.

INPUT: database selection, protein filtering, and protein maturation

Select at least one database as source for your custom Database on Demand. For each source you will be able to add filters, for most of which you can also specify a filter parameter. When specifying multiple entries in a parameter, separate them using commas.

Select a database of your choice from the drop-down menu. Then add it to your list of sources by clicking the "Add as source" button. A table showing your selected databases will appear and will allow you to add filters if you should choose so.
NOTE that the UniProt resource is split up in its components SwissProt and TrEMBL. So, in order to use all of UniProt, one has to select both databases as sources.

X

PROCESSING: enzymatic digest and ragging

After selecting the input database(s), you can now optionally specify the desired processing steps by selecting one (or more) of the predefined enzymes or defining a regular expression based enzyme of your choice. If required, you can then choose to rag the resulting peptide database.

For more detailed information please visit the User manual.

OUTPUT: post processing filters

As final processing step you can choose to restrict the results using either a powerful sequence filter or by specifying mass limits peptides. (Note: these filters are applied to the entries in the database, even if no digestion into peptides is performed)

For more detailed information please visit the User manual.

X	Filter on sequence

X	Use mass limits

from

Database on Demand

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INPUT: database selection, protein filtering, and protein maturation

PROCESSING: enzymatic digest and ragging

OUTPUT: post processing filters

TASKS: description of the entire workflow