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Nucleic Acids Research, Vol 26, Issue 12 3006-3012, Copyright © 1998 by Oxford University Press

ARTICLES

Primer design for large scale sequencing

S Haas, M Vingron, A Poustka and S Wiemann
Department of Molecular Genome Analysis and Department of Theoretical Bioinformatics,Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. shaas@dkfz_heidelberg.de

We have developed PRIDE, a primer design program that automatically designs primers in single contigs or whole sequencing projects to extend the already known sequence and to double strand single-stranded regions. The program is fully integrated into the Staden package (GAP4) and accessible with a graphical user interface. PRIDE uses a fuzzy logic-based system to calculate primer qualities. The computational performance of PRIDE is enhanced by using suffix trees to store the huge amount of data being produced. A test set of 110 sequencing primers and 11 PCR primer pairs has been designed on genomic templates, cDNAs and sequences containing repetitive elements to analyze PRIDE's success rate. The high performance of PRIDE, combined with its minimal requirement of user interaction and its fast algorithm, make this program useful for the large scale design of primers, especially in large sequencing projects.
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