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

Jakob Fredslund; Leif Schauser; Lene H Madsen; Niels Sandal; Jens Stougaard

doi:10.1093/nar/gki425

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

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W516-20. doi: 10.1093/nar/gki425.

Authors

Jakob Fredslund¹, Leif Schauser, Lene H Madsen, Niels Sandal, Jens Stougaard

Affiliation

¹ Bioinformatics 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Primers / chemistry*
Genomics / methods*
Internet
Phylogeny
Polymerase Chain Reaction*
Sequence Alignment*
Sequence Homology, Nucleic Acid
Software*
User-Computer Interface

Substances

DNA Primers