Databases and Systems

Analyzing Data in SRS with Applications
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Besides browsing query results and using direct and indirect links between databank
entries, external application programs can be used to analyze data. Typically such
applications are database searches by sequence similarity (e.g., BLAST [ 12]),
construction of multiple sequence alignments (e.g., CLUSTALW [ 13]), restriction
map analysis, and tools predicting various properties (transmembrane regions,
secondary structure, etc.).
Any system that wishes to integrate a range of applications needs to address
several complex issues. These include generating a simple to use yet extensive user
interface for each application, passing parameters to the application as well as
supplying its input data in a suitable format, and presenting the application’s results
to the user.
Application Parameters and Launching
SRS currently supports two data types: nucleotide sequences and amino acid
sequences. The system can in principle be extended to deal with any kind of data, be
it sequence alignments, sequence profiles, or even entries in a queue of dispatched
jobs. This is an area under active development.
Each entry in a set of query or link results may contain a particular data type (or
several), which could be accepted as input by certain applications. The menu next to
the ‘launch’ button on the Entry List page lists the applications that can operate on
the data types present. Selecting an application and invoking the launch button leads
to the respective ‘Application Launch’ page (see figure 3). Here one may edit the
selection of data passed to the program and set a range of parameters particular to
that application. By clicking on highlighted terms, context sensitive help can be
requested. Help is shown in one separate dedicated window, so as not to distract the
user from the main input form.