Literature DB >> 14734320

ROSO: optimizing oligonucleotide probes for microarrays.

Nancie Reymond1, Hubert Charles, Laurent Duret, Federica Calevro, Guillaume Beslon, Jean-Michel Fayard.   

Abstract

UNLABELLED: ROSO is software to design optimal oligonucleotide probe sets for microarrays. Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set. AVAILABILITY: The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors. SUPPLEMENTARY INFORMATION: http://pbil.univ-lyon1.fr/roso

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Year:  2004        PMID： 14734320     DOI： 10.1093/bioinformatics/btg401

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  27 in total

1.  ProbeLynx: a tool for updating the association of microarray probes to genes.

Authors:  Fiona M Roche; Karsten Hokamp; Michael Acab; Lorne A Babiuk; Robert E W Hancock; Fiona S L Brinkman
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

Review 2.  Microarray applications in microbial ecology research.

Authors:  T J Gentry; G S Wickham; C W Schadt; Z He; J Zhou
Journal:  Microb Ecol       Date:  2006-08-08       Impact factor: 4.552

3.  Different levels of transcriptional regulation due to trophic constraints in the reduced genome of Buchnera aphidicola APS.

Authors:  Nancie Reymond; Federica Calevro; José Viñuelas; Nicolas Morin; Yvan Rahbé; Gérard Febvay; Christian Laugier; Angela Douglas; Jean-Michel Fayard; Hubert Charles
Journal:  Appl Environ Microbiol       Date:  2006-10-13       Impact factor: 4.792

4.  Gene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose.

Authors:  Orianne Cholet; Alain Hénaut; Serge Casaregola; Pascal Bonnarme
Journal:  Appl Environ Microbiol       Date:  2007-02-16       Impact factor: 4.792

5.  Evaluating oligonucleotide properties for DNA microarray probe design.

Authors:  Xiao-Qin Xia; Zhenyu Jia; Steffen Porwollik; Fred Long; Claudia Hoemme; Kai Ye; Carsten Müller-Tidow; Michael McClelland; Yipeng Wang
Journal:  Nucleic Acids Res       Date:  2010-03-17       Impact factor: 16.971

6.  The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions.

Authors:  Sinead C Leahy; William J Kelly; Eric Altermann; Ron S Ronimus; Carl J Yeoman; Diana M Pacheco; Dong Li; Zhanhao Kong; Sharla McTavish; Carrie Sang; Suzanne C Lambie; Peter H Janssen; Debjit Dey; Graeme T Attwood
Journal:  PLoS One       Date:  2010-01-28       Impact factor: 3.240

7.  A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina.

Authors:  Frédérique Bidard; Sandrine Imbeaud; Nancie Reymond; Olivier Lespinet; Philippe Silar; Corinne Clavé; Hervé Delacroix; Véronique Berteaux-Lecellier; Robert Debuchy
Journal:  BMC Res Notes       Date:  2010-06-18

8.  BOND: Basic OligoNucleotide Design.

Authors:  Lucian Ilie; Hamid Mohamadi; Geoffrey Brian Golding; William F Smyth
Journal:  BMC Bioinformatics       Date:  2013-02-27       Impact factor: 3.169

9.  Model-based probe set optimization for high-performance microarrays.

Authors:  Germán Gastón Leparc; Thomas Tüchler; Gerald Striedner; Karl Bayer; Peter Sykacek; Ivo L Hofacker; David P Kreil
Journal:  Nucleic Acids Res       Date:  2008-12-22       Impact factor: 16.971

10.  PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.

Authors:  Athanasia Spandidos; Xiaowei Wang; Huajun Wang; Brian Seed
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971
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