SNP PrimerPicker
Yip-Kuen Lau1, Ching-Fun Lau2, Henry Yiu-Hang Fu, Hong Xue
1henryfu@ust.hk, Applied Genomics Center, Hong Kong Bioinformatics Center, ParmacoGenetics Ltd, Department of Biochemistry, Hong Kong University of Science and Technology; 2carolau@ust.hk, Applied Genomics Center, Hong Kong Bioinformatics Center, ParmacoGenetics Ltd, Department of Biochemistry, Hong Kong University of Science and Technology
The task of producing many copies of sequence segments has numerous uses. One common method to accomplish the task is by polymerase chain reaction (PCR). The design of primers is of utmost importance. Primers are short sequences that guide the copying of the required sequence. They are in the form of a pair for the two directions of copying, forward and reverse (also called left and right).
The primers are sequence segments coded the same as the region around the end of the sequence of interest. Besides this requirement, the designed primers must be dissimilar to other parts of the genome sequence. If a primer is too similar to some other parts of the genome, those parts may be replicated, in addition to the one desired. It would be even worse if both the forward and reverse direction primers have similar fragments at other locations of the genome. If both primers have matches at some other locations of the genome, these primers will drive the production of those other sequence segments as well, usually resulting in unusable outputs.
SNP PrimerPicker addresses the problem by streamlining the tedious procedure. It utilizes proven software packages as some of its components. Therefore, the quality of the system should be adequately supported. SNP PrimerPicker currently uses the well-known bl2seq to align the record to the sequence. Then Primer3 is used to design excellent primers. The primer products will then undergo similarity comparisons using BLAST client (blastcl3). Both packages are famous in generating high quality results. With SNP PrimerPicker, the flow of the complicated procedure is facilitated. The convenience ultimately brings efficiency in quality primer design.
SNP PrimerPicker was written in Perl. The user interface is self-explanatory and user friendly, thus users can start using it without the need to learn how to use it for hours. SNP PrimerPicker is a web application so that more users can access the services. The web address is bcz099.ust.hk/primerpicker.