Primer designing

Primer Blast
http://www.ncbi.nlm.nih.gov/tools/primer-blast/

1. Designs junctional primers and PCR primers. 2. Checks for primer pair specificity against the NCBI database. 3. Allows the user to check the specificity of primers against the non-targets from different organisms in a single run. 4. Allows the user to check for binding pattern between the primers and the template.

Not available

Primerquest
http://eu.idtdna.com/Scitools/Applications/Primerquest/Default.aspx

1. Designs primer for real time PCR and junctional primers. 2. Designs primers/probes for SYBR green and TaqMan.

Not available

Exon Primer
http://ihg2.helmholtz-muenchen.de/ihg/ExonPrimer.html

Designs primers to each exon region of the given target.

Not available

Quantprime
http://www.quantprime.de/

Designs junctional primers, quantitative real time PCR primers [SYBR Green real-time qPCR] and endpoint semi-quantitative-PCR primers [with or without splice variant hits].

Not available

Autoprimer
http://www.autoprime.de/AutoPrimeWeb

1. Designs RT-PCR primers. 2. Allows the user to design primers to the exon-exon border sequence.

Gunnar Wrobel1, Felix Kokocinski, and Peter Lichter. AutoPrime: selecting primers for expressed sequences. Genome Biology 2004.

2004

Did not give results when tested [as per 5th july, 2011].

Easyexon Primer
http://129.43.22.27/~primer/EasyExonPrimer.html

1. Allows the user to design primers specific to all exons or coding exons only. 2. Displays the exon sequence with SNP marking 3. Displays the binding pattern between the primers and the target.

Wu X, Munroe DJ. EasyExonPrimer: automated primer design for exon sequences. Appl Bioinformatics. 2006;5(2):119-20. PubMed PMID: 16722777.

2006

100

The source code is also available upon request. CONTACT: Xiaolin Wu (forestwu@mail.nih.gov).

ExPrimer
http://exprimer.ibab.ac.in/exprimer_html/exprimer.html

Design primer for exon junctions.

Sandhu KS, Acharya KK. ExPrimer: to design primers from exon--exon junctions. Bioinformatics. 2005 May 1;21(9):2091-2. Epub 2005 Feb 4. PubMed PMID: 15699028

2005

100

GetPrime
http://updepla1srv1.epfl.ch/getprime/

1. It a gene specific and transcript specific primer database. 2. Database covers 5 species i.e. Homo sapiens (97.5%), Mus musculus (97.9%), Caenorhabditis elegans (57.4%), Drosophila melanogaster (96.6%), Danio rerio (99.3%). 3. It is experimentally and in silico validated database.

Carine Gubelmann, Alexandre Gattiker, Andreas Massouras, Korneel Hens, Fabrice David, Frederik Decouttere, Jacques Rougemont and Bart Deplancke: GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR. Database: The Journal of Biological Databases and Curation. 2011 Sep 14;2011: bar040. PubMed PMID: 21917859; PubMed Central PMCID: PMC3173022

2011

PrimerZ
http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

1. Designs primers for exon, promoters, and human SNPs. 2. Provides chromosomal location of the gene, allows for SNP checking and avoids the regions with SNP's for primer designing. Provides promoter location also. 3. Displays the location of target gene in the chromosome and the transcript variants of the target gene [graphical representation].

Tsai MF, Lin YJ, Cheng YC, Lee KH, Huang CC, Chen YT, Yao A. PrimerZ: streamlined primer design for promoters, exons and human SNPs. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W63-5. Epub 2007 May 30. PubMed PMID: 17537812; PubMed Central PMCID: PMC1933185.

2007

100

qPrimerDepot
http://primerdepot.nci.nih.gov/

1. There are 3 unique sets of primers designed for 42,133 mouse and human RefSeq genes. 2. Over 90% of primers are designed bridging exon-exon junction. 3. Primers are designed such that they can be used for uniform annealing temperature of large high-throughput assays.

Wenwu Cui, Dennis D Taub and Kevin Gardner: qPrimerDepot: a primer database for quantitative real time PCR. Nucleic Acids Research. 2006 Sep 29;35 (1):D805-D809. PubMed PMID:17068075 ; PubMed Central PMCID: PMC1635330

2007

RExPrimer
http://www4a.biotec.or.th/rexprimer/

1. Designs junctional primers, sequencing primers, cloning primers [whole gene amplification primers can be designed without the restriction sites] and SNP primers. 2. Reports structural polymorphisms, which potentially cause PCR failure by checking target sequence with genomic variation databases.

Piriyapongsa J, Ngamphiw C, Assawamakin A, Wangkumhang P, Suwannasri P, Ruangrit U, Agavatpanitch G, Tongsima S. RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation. BMC Genomics. 2009 Dec 3;10 Suppl 3:S4. PubMed PMID: 19958502; PubMed Central PMCID: PMC2788391.

2009

100