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

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 phylogene...

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Bibliographic Details
Published in:Nucleic acids research 2005-07, Vol.33 (suppl-2), p.W516-W520
Main Authors: Fredslund, Jakob, Schauser, Leif, Madsen, Lene H., Sandal, Niels, Stougaard, Jens
Format: Article
Language:English
Subjects:
Automate
DNA Primers - chemistry
Genomics - methods
Internet
Phylogeny
Polymerase Chain Reaction
Sequence Alignment
Sequence Homology, Nucleic Acid
Software
User-Computer Interface
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gki425