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GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.

Ben Zakour N, Gautier M, Andonov R, Lavenier D, Cochet MF, Veber P, Sorokin A, Le Loir Y.

Nucleic Acids Res. 2004 Jan 2;32(1):17-24. Print 2004.


Testing of a whole genome PCR scanning approach to identify genomic variability in four different species of lactic acid bacteria.

Ben Zakour N, Grimaldi C, Gautier M, Langella P, Azevedo V, Maguin E, Le Loir Y.

Res Microbiol. 2006 May;157(4):386-94. Epub 2005 Oct 18.


[Screening of specific target sequences for the PCR detection of Staphylococcus aureus by automatic genomic comparison].

Fan Y, Zhu D, Hu Y, Shi X.

Sheng Wu Gong Cheng Xue Bao. 2011 Apr;27(4):637-44. Chinese.


Identification of Staphylococcus aureus based on PCR amplification of species specific genomic 826 bp sequence derived from a common 44-kb Sma I restriction fragment.

Stepán J, Pantůcek R, Růzicková V, Rosypal S, Hájek V, Doskar J.

Mol Cell Probes. 2001 Oct;15(5):249-57.


A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.

Charbonnier Y, Gettler B, François P, Bento M, Renzoni A, Vaudaux P, Schlegel W, Schrenzel J.

BMC Genomics. 2005 Jun 17;6:95.


Dual-genome primer design for construction of DNA microarrays.

Andersson A, Bernander R, Nilsson P.

Bioinformatics. 2005 Feb 1;21(3):325-32. Epub 2004 Aug 27.


MultiPrimer: a system for microarray PCR primer design.

Fernandes R, Skiena S.

Methods Mol Biol. 2007;402:305-14. Review.


GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags.

Varotto C, Richly E, Salamini F, Leister D.

Nucleic Acids Res. 2001 Nov 1;29(21):4373-7.


RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

Piriyapongsa J, Ngamphiw C, Assawamakin A, Wangkumhang P, Suwannasri P, Ruangrit U, Agavatpanitch G, Tongsima S.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S4. doi: 10.1186/1471-2164-10-S3-S4.


Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics.

Witney AA, Marsden GL, Holden MT, Stabler RA, Husain SE, Vass JK, Butcher PD, Hinds J, Lindsay JA.

Appl Environ Microbiol. 2005 Nov;71(11):7504-14.


PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences.

Yao J, Lin H, Van Deynze A, Doddapaneni H, Francis M, Lemos EG, Civerolo EL.

BMC Microbiol. 2008 Oct 20;8:185. doi: 10.1186/1471-2180-8-185.


Multiplex PCR strategy for subtyping the staphylococcal cassette chromosome mec type IV in methicillin-resistant Staphylococcus aureus: 'SCCmec IV multiplex'.

Milheiriço C, Oliveira DC, de Lencastre H.

J Antimicrob Chemother. 2007 Jul;60(1):42-8. Epub 2007 Apr 28. Erratum in: J Antimicrob Chemother. 2007 Sep;60(3):708.


Design and analysis of PCR primers for the amplification and cloning of human immunoglobulin Fab fragments.

de Boer M, Chang SY, Eichinger G, Wong HC.

Hum Antibodies Hybridomas. 1994;5(1-2):57-64.


LOMA: a fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens.

Lee WH, Wong CW, Leong WY, Miller LD, Sung WK.

BMC Bioinformatics. 2008 Sep 10;9:368. doi: 10.1186/1471-2105-9-368.


Primer design for Whole Genome Amplification using genetic algorithms.

Png AE, Choo KW, Lee CI, Leong SH, Kon OL.

In Silico Biol. 2006;6(6):505-14.


MPprimer: a program for reliable multiplex PCR primer design.

Shen Z, Qu W, Wang W, Lu Y, Wu Y, Li Z, Hang X, Wang X, Zhao D, Zhang C.

BMC Bioinformatics. 2010 Mar 18;11:143. doi: 10.1186/1471-2105-11-143.


Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples.

Wang G, Brennan C, Rook M, Wolfe JL, Leo C, Chin L, Pan H, Liu WH, Price B, Makrigiorgos GM.

Nucleic Acids Res. 2004 May 21;32(9):e76.


On the nature and use of randomly amplified DNA from Staphylococcus aureus.

van Leeuwen W, Sijmons M, Sluijs J, Verbrugh H, van Belkum A.

J Clin Microbiol. 1996 Nov;34(11):2770-7.

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