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Open Access Software

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

Jakob Fredslund1* and Mette Lange2

Author Affiliations

1 BiRC – Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, Building 1090, DK-8000 Århus C, Denmark

2 Research Centre Flakkebjerg, Dept. of Genetics and Biotechnology, University of Aarhus, Forsøgsvej 1, DK-4200 Slagelse, Denmark

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BMC Bioinformatics 2007, 8:369  doi:10.1186/1471-2105-8-369

Published: 3 October 2007

Abstract

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 close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds.

primique can be reached via this web address: http://cgi-www.daimi.au.dk/cgi-chili/primique/front.py webcite