GeneFisher-P - User-Level Workflow Design: A Bioinformatics Perspective - page 89

protein sequences have been submitted, a backtranslation step is also neces-
sary, where amino acid sequences are translated to a hypothetical nucleotide
sequence using either maximum redundancy methods or the codon usage of
a given organism.
Fig. 4.3 GeneFisher2 web interface
GeneFisher has been hosted as a web application at the Bielefeld Bioinfor-
matics Server (BiBiServ, [127]) for several years. Figure 4.3 shows the web
interface of its recent reimplementation, GeneFisher2 [124]: The first step in
a GeneFisher session is to provide the input sequence(s), either via file upload
or by pasting the data directly into a text field (left side of the figure). After
sequence submission the user chooses an alignment tool and the parameters.
Before consensus generation the alignment can be inspected and re-run with
adjustments, if necessary (not shown in the figure). Based on the consensus
sequence and the primer parameters, the primers are calculated (right side of
the figure). If GeneFisher can not calculate any primers for given parameters,
a rejection statistics suggests which parameters the user should change (not
shown).
4.2 GeneFisher-P Workflows
GeneFisher-P [177] is an example of a more complex workflow: PCR primer
design with the GeneFisher application comprises an alignment step in case