title: MFEprimer: multiple factor evaluation of the specificity of PCR primers.
abstract: 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 reactions. The cDNA and genomic DNA databases of 10 widely used species, as well as user custom databases, were used as DNA templates for analyzing primers specificity. Furthermore, we maintained a Primer3Plus server with a modified Primer3Manager for one-stop primer design and specificity checking.
authors.affiliation: Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing, China.
authors.forename: Wubin
authors.initials: W
authors.lastname: Qu
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Shen
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Zhao
authors.forename: Yi
authors.initials: Y
authors.lastname: Yang
authors.forename: Chenggang
authors.initials: C
authors.lastname: Zhang
mesh_terms: D019295:Computational Biology; D017931:DNA Primers / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers