The output generated by WebSat lists the sequence(s), along with the SSRs found, colored yellow and underlined, in a table format.
This is achieved by calling TROLL and, subsequently, parsing the resulting file so as to match the input parameters chosen by the user.
To help the user localize the SSR coordinates, the lines are numbered, and groups of ten bases are separated by a space. By moving the
mouse over an SSR, the user can find out its motif and length. The user can then click on any SSR to invoke a primer design program to
design a pair of primers flanking the SSR.
] was chosen as the primer design program since it is widely used and
provides a rich set of, easily modifiable, parameters. WebSat's output includes, on the top of the window, some of the main
primer3 parameter. By changing these values the user can design corresponding pair of primers flanking the SSR selected. Each time the
user clicks on an SSR, WebSat creates an input file for primer3, calls it, and parses its output file. Thanks to Ajax techniques, the
results are seamlessly integrated into the WebSat output page. If primer design is successful and a pair of primers is designed, they
are colored green along with the SSR in blue. If not, a message reporting the failure of primer design appears. When a primer sequence
overlaps with an SSR, the user can still identify the SSR, which is underlined. By providing an easy way to repeatedly change primer3
parameters, the user can make an interactive use of WebSat.
WebSat uses a session control, allowing different users to work on the site at the same time. A user can click on many SSRs, one at a
time, and each one associated with possibly different primer3 parameters. Once a SSR is selected, it is colored blue and, if the primer
design is successful, the corresponding primer information is stored in a list. At any time the user can choose to save the current list
to a CVS file. The exported file contains the following fields for each SSR: the sequence identification, SSR, product size, forward and
reverse primer sequence, melting temperature, and coordinates of the primers within the sequence. The file can be easily visualized in a
spreadsheet program, by using the option to import external data in CVS format.