- Knowledge platform
- Knowledge management
- Data integration
- Sequence analysis
- Knowledge resources
- Literature mining
- Biomax Oncology Base
- Tools
- EST analysis
- Support
- BioXM Support Web
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BioRS™ Integration and Retrieval System
Click an image for full-sized screen shot.
Database selection page
Integrated databanks are available in the databank tree which provides a convenient overview and the selection of multiple databanks for simultaneous searching. Frequently used databanks can be specified as a databank set for one-click selection. Databanks from remote BioRS installations can be included in the databank tree to allow seamless integration of data from several work sites. Users can create their own virtual databanks from search results.
BioRS sequence search
Once databanks for searching are selected, indices to be searched and search patterns are specified to perform a query. Search patterns can include wildcards and be combined with logical operators for building highly specific and complex queries.
The BioRS sequence search module allows text and keyword searches to be combined with BLAST similarity or pattern searches in a single query. Enter search criteria for sequence similarity and text fields of database entries. The following are just a few examples:
- Search with DNA or protein sequence patterns
- Search for specific EST sequences by similarity and tissue type or developmental stage
- Limit searches to a particular taxonomic group
- Specify BLAST parameters within the search
- Perform multiple alignments for selected hits
- Display alignments with color coding corresponding to the score
The algorithm used to perform the query is automatically chosen depending on the type of input sequences and database sequences specified for the search.
BioRS search results
Search results provide a choice of views for sequences, including graphical and FASTA formats. They are displayed in a table listing the databank in which the result was found, the entry identifier and any other elements that were selected to be displayed in the results. An individual entry can be examined by clicking the entry identifier.
Excerpt from a BioRS view of a UniProt entry
Several display options allow selected information from search results and returned entries to be viewed and sorted. Returned information can be viewed in the original, XML or FASTA format. When enabled, entries can be viewed with user-defined criteria or external applications. Specific subsets of search results can be selected for downloading, adding to the clipboard or passing to external applications. External applications can be seamlessly integrated into the BioRS system, allowing results to be used by the application directly.
Comfortable work environment
Both queries and search results can be saved in an individual archive for subsequent reuse or modification. Researchers can define their individual work environment with pre-selected sets of databases and user-specific views. Queries and environment customization can be made available to all users.