Objective: Most bioinformatics applications that design primers for the technique of the PCR analyze one single sequence of DNA as template; only a few applications process various nucleotide sequences. A common feature of existing software is that produces primers that are unique for each template, which is partially useful in the genomic analysis. The objective was to create an application able to find the primers that are identical in multiple nucleotide sequences and the primers that are unique to each sequence.
Methods: I applied object-oriented programming using the C++ Builder 2009 to implement algorithms that find particular short strings (primers) in nucleotide sequences. The software is a set of applications with a simple design that serves as a didactic tool to find and analyze primers. To test the application, I used molecular biology to clone genes in the laboratory.
Results: I have developed a bioinformatics application for the PCR technology named SQPrimer that focus in finding identical primers in several sequences of nucleotides. I have shown the applicability and accuracy of the application in various examples of the genetic analysis. The software was able to 1: design primers at conserved sequences of nucleotides among different species; 2: find and design mutation specific primers in sequences with single nucleotide polymorphisms and 3: design primers to detect length polymorphisms: insertions, deletions or expansion of triplet nucleotide repeats.
Conclusion: SQPrimer is bioinformatics software that adds the capability of designing primers that are identical in a batch of sequences, a utility that can be used in some strategies of the PCR analysis. The software is accessible at http://www2.uah.es/biologia_celular/JPM/SQPP/SQPrimer.html.