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 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.
Fredslund
Jakob
J
Bioinformatics Research Center, University of Aarhus, Hoegh-Guldbergsgade 10, 8000 Aarhus C, Denmark. jakobf@birc.au.dk
Schauser
Leif
L
Madsen
Lene H
LH
Sandal
Niels
N
Stougaard
Jens
J
D017931:DNA Primers / Q000737:chemistry*; D023281:Genomics / Q000379:methods*; D020407:Internet; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers