MFEprimer-3.0: quality control for PCR primers.
Nucleic Acids Res
; 47(W1): W610-W613, 2019 07 02.
Article
en En
| MEDLINE
| ID: mdl-31066442
ABSTRACT
Quality control (QC) for lab-designed primers is crucial for the success of a polymerase chain reaction (PCR). Here, we present MFEprimer-3.0, a functional primer quality control program for checking non-specific amplicons, dimers, hairpins and other parameters. The new features of the current version include (i) more sensitive binding site search using the updated k-mer algorithm that allows mismatches within the k-mer, except for the first base at the 3' end. The binding sites of each primer with a stable 3' end are listed in the output; (ii) new algorithms for rapidly identifying self-dimers, cross-dimers and hairpins; (iii) the command-line version, which has an added option of JSON output to enhance the versatility of MFEprimer by acting as a QC step in the 'primer design â quality control â redesign' pipeline; (iv) a function for checking whether the binding sites contain single nucleotide polymorphisms (SNPs), which will affect the consistency of binding efficiency among different samples. In summary, MFEprimer-3.0 is updated with the well-tested PCR primer QC program and it can be integrated into various PCR primer design applications as a QC module. The MFEprimer-3.0 server is freely accessible without any login requirement at https//mfeprimer3.igenetech.com/ and https//www.mfeprimer.com/. The source code for the command-line version is available upon request.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
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Reacción en Cadena de la Polimerasa
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Cartilla de ADN
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2019
Tipo del documento:
Article
País de afiliación:
China