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

TY - JOUR

T1 - PriFi - Using a Multiple Alignment of Related Sequences to Find Primers for  Amplification of Homologs

AU - Fredslund, Jakob

AU - Schauser, Leif

AU - Madsen, Lene Heegaard

AU - Sandal, Niels Nørgaard

AU - Stougaard, Jens

N1 - Jakob Fredslund, Leif Schauser, Lene Heegard Madsen, Niels Sandal, Jens Stougaard, PriFi - Using a Multiple Alignment of Related Sequences to Find Primers for Amplification of Homologs, Nucleic Acids Research 2005 33(Web Server issue):W516-W520; doi:10.1093/nar/gki425

PY - 2005

Y1 - 2005

N2 - 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. <!-- null -->

AB - 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. <!-- null -->

M3 - Journal article

SN - 0305-1048

VL - 33

SP - 516

EP - 520

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - W

ER -