Abstract
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.
Highlights
Primers are a short chain of nucleotides chemically synthesized in orientation 5’ to 3’ that are used for amplification of DNA by the polymerase chain reaction (PCR)
The steps to clone the CLRP cDNA of CHO cells was as follows: 1-To obtain the human cDNA, 2-To use of SQPrimer to design the primers that are identical in the rat and human sequences, 3-To use different combinations of those homologous primers in PCRs using the cDNA of CHO cells as template. 4-To isolate and purify the PCR products in the agarose gels and clone that cDNA
SQPrimer showed to be useful to clone the CLRP cDNA of CHO cells; the results indirectly show that CLRP is a conserved gene in vertebrates because the homology of sequence of their primers
Summary
Primers are a short chain of nucleotides chemically synthesized in orientation 5’ to 3’ that are used for amplification of DNA by the polymerase chain reaction (PCR). Many genetic applications use the PCR; among them, those that detect variations in the nucleotide sequence of genes. PCR is used in the analysis of mutations involved in genetic diseases, in forensics and in the studies of differences amongst species. There are several software programs in the web that design specific primers for the PCR [3,4,5,6,7,8]. That particular software has an array of different applications; for instance, it designs degenerated primers, finds primers that recognize microsatellites of nucleotide repeats (or SSR, simple sequence repeat) or detects primers that include single nucleotide polymorphism (SNP), a kind of nucleotide variation in the DNA. The existing software has in common that they serve to design primers that are different and specific for one or various DNA templates
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
