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GeneFisher-P
This second application scenario is based on the GeneFisher web application
for PCR primer design [109, 124]. To provide a more flexible alternative to the
monolithic web application, it has been realized as Bio-jETI workflow. With
the resulting GeneFisher-P [177], workflow variants that are not covered by
the web application, such as using alternative services for individual analysis
steps or batch processing of input data sets, can easily be built at the user
level.
4.1 Background: PCR Primer Design
A key technology within the discipline of genetic engineering and one of the
most widely used techniques in biological laboratories today is the polymerase
chain reaction (PCR) [338], developed around 1985. It can be pictured as “a
kind of genetic photocopying” [55, p. 291]: it allows for isolating and expo-
nentially amplifying short fragments from a DNA sequence (up to around
6000 bp) without utilizing living cells for the reproduction. Analysis of ge-
netic information is only possible when a sucient amount of (identical) DNA
is available, and so PCR is used in biological research projects (for instance
for DNA sequencing and functional analysis of genes), and medicine (diagno-
sis of hereditary diseases, detection of genetic defects), as well as in forensic
sciences and paternity testing (identification of genetic fingerprints).
4.1.1 Polymerase Chain Reaction
A PCR run consists of a series of cycles (usually 30-60) which are essentially
carried out in three steps (see Figure 4.1):
1. The denaturation step melts the double-stranded DNA into two separate
strands at a temperature of 94-96 C. In the first cycle, this steps needs
 
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