GeneFisher-P - User-Level Workflow Design: A Bioinformatics Perspective - page 91

• DCA [312] stands for Divide-and-Conquer Multiple Sequence Alignment .

The program is very fast and produces high-quality multiple sequence
alignments of protein, RNA, or DNA sequences. It is also provided as a
web service at BiBiServ.

•

BatCons is one of the mentioned legacy programs from the original Gene-
Fisher project. It performs backtranslation (in case of protein sequences)
and consensus calculation (if the input consists of multiple sequences).

•

gf 2000 , another legacy program, is responsible for the actual primer
design. The input has to be a single nucleotide sequence.

Local tasks like input validation, user interaction and the definition of the
control flow, which are programmed in the case of GeneFisher, are modeled in
GeneFisher-P by jABC Common-SIBs that encapsulate corresponding func-
tionality. For the control flow, these are mainly SIBs declaring variables or
checking conditions, as well as for steering the flow of control in dependence
of intermediate results. User interaction refers, for instance, to SIBs for file
management and data input, as well as for display of (intermediate) results.
In the GeneFisher web applications, the user can choose between ClustalW
and DCA for the multiple alignment. For simplicity, the GeneFisher-P work-
flows are modeled using only the ClustalW service. However, analogously to
what has already been shown for the previous scenario, ClustalW can easily
be exchanged with DCA by the user.

4.2.2 Interactive GeneFisher-P Workflow

Different workflow realizations of the GeneFisher process as summarized in
Figure 4.4 have been built in the scope of the GeneFisher-P project. Figure
4.5 shows a simple interactive version: The workflow starts with asking the
user for a single input sequence file and a classification of the sequences
(i.e., single or multiple sequence, nucleotide or amino acid). According to the
sequence type, an appropriate primer design subworkflow is called. Finally,
the result of the primer design is stored into a file specified by the user.

Fig. 4.5 Interactive GeneFisher-P workflow