MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity
نویسندگان
چکیده
منابع مشابه
MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity
Evaluating the specificity of polymerase chain reaction (PCR) primers is an essential step in PCR primer design. The MFEprimer-2.0 server allows users to check primer specificity against genomic DNA and messenger RNA/complementary DNA sequence databases quickly and easily. MFEprimer-2.0 uses a k-mer index algorithm to accelerate the search process for primer binding sites and uses thermodynamic...
متن کاملMFEprimer: multiple factor evaluation of the specificity of PCR primers
SUMMARY We developed a program named MFEprimer for evaluating the specificity of PCR primers based on multiple factors, including sequence similarity, stability at the 3'-end of the primer, melting temperature, GC content and number of binding sites between the primer and DNA templates. MFEprimer can help the user to select more suitable primers before running either standard or multiplex PCR r...
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Multiplex PCR method is a powerful technology as a potent tool to amplify specific DNA fragments from genomic DNA using Taq DNA polymerase and primer sets. Since multiple reactions occur in single tube, multiplex PCR has the potential to produce considerable savings of time and effort. Its applications are widely ranged from in vitro cloning of specific regions of DNA to diagnosis of disease [1...
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A novel primer designed to improve the specificity of PCR amplification, called the annealing control primer (ACP), comprises a tripartite structure with a polydeoxyinosine [poly(dI)] linker between the 3' end target core sequence and the 5' end nontarget universal sequence. We show that this ACP linker prevents annealing of the 5' end nontarget sequence to the template and facilitates primer h...
متن کاملSelecting specific PCR primers with MFEprimer.
Selecting specific primers is crucial for polymerase chain reaction (PCR). Nonspecific primers will bind to unintended genes and result in nonspecific amplicons. MFEprimer is a program for checking the specificity of PCR primers against the background DNA. In this chapter, we introduce: (1) the factors that affect the specificity of primers; (2) the principle of MFEprimer and its settings; (3) ...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2012
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gks552