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

@article{citeulike:3013828, 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.}, address = {Bioinformatics Research Center, University of Aarhus, Hoegh-Guldbergsgade 10, 8000 Aarhus C, Denmark. jakobf@birc.au.dk}, author = {Fredslund, J. and Schauser, L. and Madsen, L. H. and Sandal, N. and Stougaard, J. }, citeulike-article-id = {3013828}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {alignment, pcr, primer}, month = {July}, number = {Web Server issue}, posted-at = {2008-07-17 09:09:39}, priority = {2}, title = {PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/15980525}, volume = {33}, year = {2005} }

TY - JOUR ID - citeulike:3013828 L3 - citeulike-article-id:3013828 TI - PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. JF - Nucleic acids research VL - 33 IS - Web Server issue AD - Bioinformatics Research Center, University of Aarhus, Hoegh-Guldbergsgade 10, 8000 Aarhus C, Denmark. jakobf@birc.au.dk SN - 1362-4962 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. KW - alignment KW - pcr KW - primer AU - Fredslund, J AU - Schauser, L AU - Madsen, LH AU - Sandal, N AU - Stougaard, J PY - 2005/07/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/15980525 ER -