ROSO: optimizing oligonucleotide probes for microarrays

被引：46

作者：

Reymond, N ^{[1
]}

Charles, H

Duret, L

Calevro, F

Beslon, G

Fayard, JM

机构：

[1] Inst Natl Sci Appl, UMR INRA, Biol Fonct Insectes & Interact BF21, F-69621 Villeurbanne, France

[2] Univ Lyon 1, UMR CNRS, BBE, F-69622 Villeurbanne, France

[3] PRISMa, F-69621 Villeurbanne, France

来源：

BIOINFORMATICS | 2004年 / 20卷 / 02期

关键词：

D O I：

10.1093/bioinformatics/btg401

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Summary: ROSO is software to design optimal oligonucleotide probe sets for microarrays. Selected probes show no significant cross-hybridization, no stable secondary structures and their T-m are chosen to minimize the T-m variability of the probe set.

引用

页码：271 / 273

页数：3

共 15 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] CHARACTERIZATION OF RNA HAIRPIN LOOP STABILITY [J].

GROEBE, DR ;

UHLENBECK, OC .

NUCLEIC ACIDS RESEARCH, 1988, 16 (24) :11725-11735

[3] Options available - from start to finish - for obtaining data from DNA microarrays [J].

Holloway, AJ ;

van Laar, RK ;

Tothill, RW ;

Bowtell, DDL .

NATURE GENETICS, 2002, 32 (Suppl 4) :481-489

[4] Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer [J].

Hughes, TR ;

Mao, M ;

Jones, AR ;

Burchard, J ;

Marton, MJ ;

Shannon, KW ;

Lefkowitz, SM ;

Ziman, M ;

Schelter, JM ;

Meyer, MR ;

Kobayashi, S ;

Davis, C ;

Dai, HY ;

He, YDD ;

Stephaniants, SB ;

Cavet, G ;

Walker, WL ;

West, A ;

Coffey, E ;

Shoemaker, DD ;

Stoughton, R ;

Blanchard, AP ;

Friend, SH ;

Linsley, PS .

NATURE BIOTECHNOLOGY, 2001, 19 (04) :342-347

[5] Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays [J].

Kane, MD ;

Jatkoe, TA ;

Stumpf, CR ;

Lu, J ;

Thomas, JD ;

Madore, SJ .

NUCLEIC ACIDS RESEARCH, 2000, 28 (22) :4552-4557

[6] Selection of optimal DNA oligos for gene expression arrays [J].

Li, FG ;

Stormo, GD .

BIOINFORMATICS, 2001, 17 (11) :1067-1076

[7] Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays [J].

Nielsen, HB ;

Wernersson, R ;

Knudsen, S .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3491-3496

[8] An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification [J].

Pozhitkov, AE ;

Tautz, D .

BMC BIOINFORMATICS, 2002, 3 (1)

[9] Genome-wide expression profiling in Escherichia coli K-12 [J].

Richmond, CS ;

Glasner, JD ;

Mau, R ;

Jin, HF ;

Blattner, FR .

NUCLEIC ACIDS RESEARCH, 1999, 27 (19) :3821-3835

[10] OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach [J].

Rouillard, JM ;

Zuker, M ;

Gulari, E .

NUCLEIC ACIDS RESEARCH, 2003, 31 (12) :3057-3062

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