Netprimer

{{Short description|Web-based tool for analysing primers used in PCR to amplify a DNA sequence}}

{{Infobox software

| name = NetPrimer

| logo =

| screenshot =

| caption =

| developer = Premier Biosoft

| latest release version = 1.10{{citation needed|date=February 2017}}

| latest release date = 6 May 2002{{citation needed|date=February 2017}}

| latest preview version =

| latest preview date =

| operating system =

| platform = Java applethttp://www.premierbiosoft.com/netprimer/netprlaunch/Help/xnetprlaunch.html (although it says "requires Java plug-in 1.4 or later for Windows", further down the page it also shows they've tested it on Mac OS X)

| genre = Bioinformatics

| license = commercial

| website = http://www.premierbiosoft.com/netprimer/

}}

NetPrimer is a gratis web-based tool used for analysing primers used in PCR to amplify a DNA sequence.{{Cite web |url=http://www.ebd.csic.es/andy/MolEcolNotes05.pdf |title=Archived copy |access-date=2009-01-07 |archive-date=2009-12-14 |archive-url=https://web.archive.org/web/20091214141622/http://www.ebd.csic.es/andy/MolEcolNotes05.pdf |url-status=dead }} The software predicts the melting temperature of the primers using the nearest neighbor thermodynamic algorithm. The accurate prediction of the melting temperature (Tm) is one of the most important factors that governs the success of a PCR reaction.{{cite book|title=PCR Primer: A Laboratory Manual, Second Edition (2003) Paperback |author1=Dieffenbach, C.W.|author2=Dveksler, G.S.|date=2003|publisher=Cold Spring Harbor Laboratory Press|isbn=9780879696542|url=https://books.google.com/books?id=IbAcGxyD06MC|page=61|accessdate=2015-05-17}}

NetPrimer also analyzes the thermodynamically important secondary structures such as hairpins, self and cross dimers, runs and repeats.pga.mgh.harvard.edu/primerbank/help.html These structures significantly affect the primer efficiency and therefore the success{{clarify|date=February 2017}} of a PCR reaction.

NetPrimer can be used to determine the best primer pairs for a given set of experimental conditions. The program assigns a rating to each primer analyzed.{{Cite web |url=http://www.aphis.usda.gov/wildlife_damage/nwrc/publications/08pubs/piaggio081.pdf |title=Archived copy |access-date=2009-01-07 |archive-date=2009-01-10 |archive-url=https://web.archive.org/web/20090110112804/http://www.aphis.usda.gov/wildlife_damage/nwrc/publications/08pubs/piaggio081.pdf |url-status=dead }} The rating is based on the proximity of the thermodynamic parameters to their ideal scores.

In addition to the primer quality, its molecular weight and optical activity (both in nmol/A260 and μg/A260) are also presented for quantitation. Primers are analyzed for their GC% (Guanine-Cytosine content).{{Cite journal|url=http://jcm.asm.org/cgi/reprint/39/11/4119.pdf|doi=10.1128/JCM.39.11.4119-4124.2001|title=Development and Evaluation of Serotype- and Group-Specific Fluorogenic Reverse Transcriptase PCR (Taq Man) Assays for Dengue Virus|year=2001|last1=Callahan|first1=Johnny D.|last2=Wu|first2=Shuenn-Jue L.|last3=Dion-Schultz|first3=Amanda|last4=Mangold|first4=Beverly E.|last5=Peruski|first5=Leonard F.|last6=Watts|first6=Douglas M.|last7=Porter|first7=Kevin R.|last8=Murphy|first8=Gerald R.|last9=Suharyono|first9=Wuryadi|last10=King|first10=Chwan-Chuen|last11=Hayes|first11=Curtis G.|last12=Temenak|first12=Joseph J.|journal=Journal of Clinical Microbiology|volume=39|issue=11|pages=4119–4124|pmid=11682539|pmc=88496}} This important parameter determines their annealing strength.