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Nucleic Acids Research 2005 33(Web Server Issue):W516-W520; doi:10.1093/nar/gki425
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs

Jakob Fredslund*, Leif Schauser, Lene H. Madsen1, Niels Sandal1 and Jens Stougaard1

Bioinformatics Research Center, University of Aarhus Hoegh-Guldbergsgade 10, 8000 Aarhus C, Denmark 1Laboratory of Gene Expression, Department of Molecular Biology, University of Aarhus Gustav Wieds Vej 10, 8000 Aarhus C, Denmark

*To whom correspondence should be addressed. Tel: +45 8942 3125; Fax: +45 8942 3077; Email: jakobf{at}birc.au.dk

Received February 2, 2005. Revised March 15, 2005. Accepted March 23, 2005.

Using a comparative approach, the web program PriFi (http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main) designs pairs of primers useful for PCR amplification of genomic DNA in species where prior sequence information is not available. The program works with an alignment of DNA sequences from phylogenetically related species and outputs a list of possibly degenerate primer pairs fulfilling a number of criteria, such that the primers have a maximal probability of amplifying orthologous sequences in other phylogenetically related species. Operating on a genome-wide scale, PriFi automates the first steps of a procedure for developing general markers serving as common anchor loci across species. To accommodate users with special preferences, configuration settings and criteria can be customized.


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