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A comparative account of primer designing resources, feature-validations and application-based categorizations : SNP primers
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
Yao J, Lin H, Van Deynze A, Doddapaneni H, Francis M, Lemos EG, Civerolo EL. PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences. BMC Microbiol. 2008 Oct 20;8:185. PubMed PMID: 18937861; PubMed Central PMCID: PMC2579435.

"URL is not working [as per 6th July 2011]. Unable to access the tool. Not yet validated. But general features are written as claimed by the author. See ""Feature table"" for the description of the tool."
1. Web-based Allele Specific Primer [WASP] designs allele-specific (AS) primers for detecting SNPs and mutations.
Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S. WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics. 2007 Aug 14;8:275. PubMed PMID: 17697334; PubMed Central PMCID: PMC1976135.
1. PrimerBank is a public resource of primers designed for gene expression detection or quantification using real-time PCR. 2. There are primers covering almost all genes of mouse and human. 3. Database is validated using 26,855 primer pairs for 27,681 genes of mouse.
Xiaowei Wang, Athanasia Spandidos, Huajun Wang and Brian Seed: PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Research. 2011 Oct 21;40(D1): D1144-D1149. PubMed PMID: 22086960; PubMed Central PMCID: PMC3245149

There are two older version of this database. One is 2003 version and other is 2010 version
Array Designer
Allows the user to input multiple targets and designs probes for gene expression profiling and SNP detection.
Not available
Not available

Features are written as claimed by the author. Not validated completely.
1. Allows the user to input multiple set of sequences. It will take maximum of 500 sequences at a time to process. 2. It has the primer parameters similar to primer 3. 3. Designs several types of primers including generic primers for any DNA sequences, hybridization oligos, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. 4. Mis-priming library is available for plants only.
You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 2008 May 29;9:253. PubMed PMID: 18510760.

Very fast working tool.
Beacon Designer
1. Designs primer for Beacon, SYBR green, TaqMan, HRMA [high resolution melting analysis], methyl light TaqMan, and scorpions. 2. Allows the user to view and reuse the pre-search query. 3. Allows the user to add SNP/Point mutation manually. 4. Allows the user to set the reaction condition such as salt concentration, primer concentration etc. 5. Allows the user to open dbSNP directly from the tool.
Not available
Not available
Conserved Primers 2.0
Designs intron flanking primers [i.e. primers that span the intron sequence] for the plants such as Oriyza sativa, Sorghum bicolour, Barchypodium distachyon, Arabindopsis thaliana, Glycine max etc.
You FM, Huo N, Gu YQ, Lazo GR, Dvorak J, Anderson OD. Conserved Primers 2.0: a high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery. BMC Bioinformatics. 2009 Oct 13;10:331. PubMed PMID: 19825183.
dCAPS Finder
1. Designs primers for SNP analysis. 2. Also designs mis-matched PCR primers to create or remove recognition sites.
Neff MM, Turk E, Kalishman M. Web-based primer design for single nucleotide polymorphism analysis. Trends Genet. 2002 Dec;18(12):613-5. PubMed PMID:12446140.
1. Involves in designing probes to detect large number of SNPs and helps in identifying microbial subtypes. 2. Designs oligonucleotide probes targeting microbial or other genomes. This probe is a linear oligonucleotide with target-complementary sequences at the ends and a non-complementary linking segment in between.
Thiyagarajan S, Karhanek M, Akhras M, Davis RW, Pourmand N. PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens. BMC Bioinformatics. 2006 Nov 14;7:500. PubMed PMID: 17105657.

Features are written as claimed by the author. Not validated completely.
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.
Designs primers for SNP genotyping, mutagenic study etc.
Chang HW, Chuang LY, Cheng YH, Hung YC, Wen CH, Gu DL, Yang CH. Prim-SNPing: a primer designer for cost-effective SNP genotyping. Biotechniques. 2009 May;46(6):421-31. PubMed PMID: 19480636.

Features are written as claimed by the author. Not validated completely.
1. Designs Junction 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.
Weckx S, De Rijk P, Van Broeckhoven C, Del-Favero J. SNPbox: a modular software package for large-scale primer design. Bioinformatics. 2005 Feb 1;21(3):385-7. Epub 2004 Sep 3. PubMed PMID: 15347573.

Not yet identified the unique feature of the tool. Features are written as claimed by the author. Refer Feature Table for the detail description of the tool.
1. It is a database that holds primers and probes used for real time PCR assay. 2. There are 8606 real time PCR assays detailing 5928 genes.
Steve Lefever, Jo Vandesompele, Frank Speleman and Filip Pattyn: RTPrimerDB: the portal for real-time PCR primers and probes. Nucleic Acids Research. 2008 Oct 8;37(1):D942-D945. PubMed PMID: 18948285; PubMed Central PMCID: PMC2686610

There are two older version of this database. One is 2003 version and other is 2006 version
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