Primique: automatic design of specific PCR primers for each sequence in a family

Background: In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains. Results: This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences not to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming. Conclusion: Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any clo...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Jakob Fredslund, Mette Lange
• Keywords: BMCBI 2007, Sequences, Specific Primers, Target Sequence