PriFi - Using a Multiple Alignment of Related Sequences to Find Primers for  Amplification of Homologs

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  • Bioinformatics Research Centre (BiRC)
  • Department of Molecular Biology
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.
Original languageEnglish
JournalNucleic Acids Research
Volume33
IssueW
Pages (from-to)516-520
Number of pages5
ISSN0305-1048
Publication statusPublished - 2005

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