SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation
Figure 1
Flow-chart
showing the functional structure of SSR Locator. (A) Perl script to search SSRs;
(B) text file where information from detected SSRs is stored; (C) module for the
statistical calculations for SSR motif occurrence; (D) module that formats text
files into standard Primer3 input files; (E) running of Primer3; (F) module for
running Virtual-PCR (using a second sequence file as a template); (G) module
performing global alignment between homologous amplicons; (H) identity and
alignment score calculations between homologous amplicons; and (I) file
containing SSR, primer, homologous amplicons, identity, and score information.