BrEPS webservice help
This page provides a complete overview of the features of the BrEPS webservice (BrEPSweb).
There are two ways to search the BrEPS database:
The sequence search is the main functionality of the BrEPS webservice. The search form is located on the main page. Three input formats are supported:
Plain amino acid or DNA sequence string
Amino acid or DNA sequence in FASTA format
UniProtKB accession (amino acid sequence is automatically retrieved from UniProt)
After submitting the sequence, the BrEPS search starts. You will be redirected to your unique results page, where the results of your search will be displayed after completion. The unique ID of your request can be saved for future results retrieval.
On the upper part of the results page the input sequence is shown. The lower part of
the results page is a list of all pattern matches for the input sequence. Hovering
over a result entry shows where the pattern matches the input sequence as well as the
position and length of the hit. Basic informations of the pattern are provided in the
list, for further details the BrEPS ID
BPxxxxxx can be clicked to show the
BrEPSweb only supports one input sequence at a time. For batch analysis of multiple sequences you can use the BrEPS command line tool (BrEPScmd)
The fulltext search can be used to search the BrEPS database for patterns with a specific enzymatic function or for patterns for a specific enzyme. The search form is also located on the main page and can be found directly below the sequence search field. The fulltext search can be used to search UniProtKB accessions, EC numbers or the proposed function using the IUBMB enzyme nomenclature.
The results of the search will be shown as a list of patterns, providing basic informations about the patterns. The search results can be sorted by BrEPS ID or E-value. Further details for the pattern can be shown by visiting the pattern page.
BrEPSweb pattern pages
Every pattern is annotated based on the sequences it was created from. BrEPS proposes a function based on the UniProtKB EC number annotation of every sequence used to generate the pattern. Additionally, values from the clustering (E-value, cluster ID and node ID) are shown. To complete the annotation, every single EC number and all associated UniProtKB accessions are displayed. The created patterns (standard pattern and if generated the extended pattern) are shown and can be displayed in PROSITE and regular expression format.
Alternatively, the annotation page can be shown in a flatfile format, which is similar to the UniProtKB flatfile format. The data fields are identified by a two letter ID, followed by a defined line of content. A full list of identifiers and the syntax of the flatfile can be found here. A link to the flatfile view can be found below right of the pattern ID.
BrEPSweb pattern list
All BrEPS patterns can be browsed using the pattern list. On multiple pages, all present patterns are listed and can be sorted by BrEPS ID and E-value.
The download page allows the download of the BrEPS command line tool for batch analysis of sequences. Additionally the BrEPS database can be downloaded for usage with the command line tool.