Abstract
Primer design represents a widely employed gambit in diverse molecular applications including PCR, sequencing, and probe hybridization. Variations of PCR, including primer walking, allele-specific PCR, and nested PCR provide specialized validation and detection protocols for molecular analyses that often require screening large numbers of DNA fragments. In these cases, automated sequence retrieval and processing become important features, and furthermore, a graphic that provides the user with a visual guide to the distribution of designed primers across targets is most helpful in quickly ascertaining primer coverage. To this end, I describe here, PrimerMapper, which provides a comprehensive graphical user interface that designs robust primers from any number of inputted sequences while providing the user with both, graphical maps of primer distribution for each inputted sequence, and also a global assembled map of all inputted sequences with designed primers. PrimerMapper also enables the visualization of graphical maps within a browser and allows the user to draw new primers directly onto the webpage. Other features of PrimerMapper include allele-specific design features for SNP genotyping, a remote BLAST window to NCBI databases, and remote sequence retrieval from GenBank and dbSNP. PrimerMapper is hosted at GitHub and freely available without restriction.
Highlights
PCR is a widely employed and indispensable tool for an extensive and ever-growing number of molecular applications[1]
PrimerMapper will be helpful for researchers working with large datasets where primers must be efficiently designed for many genes or SNPs, as well as for various PCR-based applications including primer walking, nested PCR, sequence-specific probe construction, and assembly PCR reactions, where graphical outputs can quickly help users determine primer distribution
PrimerMapper can automate sequence retrieval and primer design for any number of sequences while returning maps of primers along each sequence that can be visualized as image files or within a browser
Summary
PCR is a widely employed and indispensable tool for an extensive and ever-growing number of molecular applications[1]. When designing primers for large numbers of sequences, automated sequence retrieval and processing becomes important, and graphical outputs depicting the map of sequence/primer position is often the best way to rapidly validate primer coverage and distribution. PrimerMapper will be helpful for researchers working with large datasets where primers must be efficiently designed for many genes or SNPs, as well as for various PCR-based applications including primer walking, nested PCR, sequence-specific probe construction, and assembly PCR reactions, where graphical outputs can quickly help users determine primer distribution
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.
