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Items: 1 to 20 of 89

1.

An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region.

Sahu M, Sahu J, Sahoo S, Dehury B, Sarma K, Sarmah R, Sen P, Modi MK, Barooah M.

Bioinformation. 2012;8(4):181-4. doi: 10.6026/97320630008181. Epub 2012 Feb 28.

2.

A new method for designing degenerate primers and its use in the identification of sequences in Brachiaria showing similarity to apomixis-associated genes.

Gorrón E, Rodríguez F, Bernal D, Rodriguez-Rojas LM, Bernal A, Restrepo S, Tohme J.

Bioinformatics. 2010 Aug 15;26(16):2053-4. doi: 10.1093/bioinformatics/btq312. Epub 2010 Jun 14.

PMID:
20547638
3.

CODEHOP PCR and CODEHOP PCR primer design.

Staheli JP, Boyce R, Kovarik D, Rose TM.

Methods Mol Biol. 2011;687:57-73. doi: 10.1007/978-1-60761-944-4_5.

PMID:
20967601
4.

Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm.

Yang CH, Chang HW, Ho CH, Chou YC, Chuang LY.

PLoS One. 2011 Mar 18;6(3):e17729. doi: 10.1371/journal.pone.0017729.

5.

Amplification of orthologous genes using degenerate primers.

Chakravorty S, Vigoreaux JO.

Methods Mol Biol. 2010;634:175-85. doi: 10.1007/978-1-60761-652-8_13.

PMID:
20676984
6.

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.

7.

Degenerate primer design via clustering.

Wei X, Kuhn DN, Narasimhan G.

Proc IEEE Comput Soc Bioinform Conf. 2003;2:75-83.

PMID:
16452781
8.

Flexgrepps--flexible greedy peptide pool search: computation of near-optimal sets of degenerate polypeptides for antigenic screening.

Krivan W, Arnold N, Morales C, Carter D.

J Bioinform Comput Biol. 2012 Oct;10(5):1250009. doi: 10.1142/S0219720012500096. Epub 2012 Jun 22.

PMID:
22849364
9.

Role of the ruvB gene in homologous and homeologous recombination in Rhizobium etli.

Martinez-Salazar JM, Romero D.

Gene. 2000 Feb 8;243(1-2):125-31.

PMID:
10675620
10.

Genomic multiple sequence alignments: refinement using a genetic algorithm.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2005 Aug 8;6:200.

11.

QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments.

Kim N, Lee C.

Bioinformatics. 2007 Sep 1;23(17):2331-3. Epub 2007 Jun 28.

PMID:
17599926
12.

UniPrime2: a web service providing easier Universal Primer design.

Boutros R, Stokes N, Bekaert M, Teeling EC.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W209-13. doi: 10.1093/nar/gkp269. Epub 2009 Apr 28.

13.

Rhizobium tropici response to acidity involves activation of glutathione synthesis.

Muglia CI, Grasso DH, Aguilar OM.

Microbiology. 2007 Apr;153(Pt 4):1286-96.

PMID:
17379738
14.

ConservedPrimers 2.0: a high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery.

You FM, Huo N, Gu YQ, Lazo GR, Dvorak J, Anderson OD.

BMC Bioinformatics. 2009 Oct 13;10:331. doi: 10.1186/1471-2105-10-331.

15.

Designing multiple degenerate primers via consecutive pairwise alignments.

Najafabadi HS, Torabi N, Chamankhah M.

BMC Bioinformatics. 2008 Jan 27;9:55. doi: 10.1186/1471-2105-9-55.

16.

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments.

Jabado OJ, Palacios G, Kapoor V, Hui J, Renwick N, Zhai J, Briese T, Lipkin WI.

Nucleic Acids Res. 2006;34(22):6605-11. Epub 2006 Nov 28.

17.

HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.

Le T, Altman T, Gardiner K.

Bioinformatics. 2010 Feb 1;26(3):302-9. doi: 10.1093/bioinformatics/btp676. Epub 2009 Dec 8.

PMID:
19996163
18.

BatchPrimer3: a high throughput web application for PCR and sequencing primer design.

You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD.

BMC Bioinformatics. 2008 May 29;9:253. doi: 10.1186/1471-2105-9-253.

19.

Searching for nitrile hydratase using the Consensus-Degenerate Hybrid Oligonucleotide Primers strategy.

Lourenço PM, Almeida T, Mendonça D, Simões F, Novo C.

J Basic Microbiol. 2004;44(3):203-14.

PMID:
15162394
20.

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design.

Rose TM, Henikoff JG, Henikoff S.

Nucleic Acids Res. 2003 Jul 1;31(13):3763-6.

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