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Updated: Aug 2, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
Published on: September 3, 2009
PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs
Jakob Fredslund1, Leif Schauser, Lene H Madsen
1Bioinformatics Research Center, University of Aarhus, Hoegh-Guldbergsgade 10, 8000 Aarhus C, Denmark. jakobf@birc.au.dk
Abstract:
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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