|  | ROSO
a friend for your designBBE contribution to PBIL in Lyon, France |  |
| Articles |
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Reymond, N., Charles, H., Duret, L., Calevro, F., Beslon, G. and Fayard, J.-M. (2004). ROSO: Optimizing Oligonucleotide Probes for Microarrays. Bioinformatics., 20(2):271-273. |
 | Journal of Microbiological Methods |
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Calevro, F., Charles, H, Reymond, N., Dugas, V., Cloarec, J.-P., Bernillon, J., Rahbé, Y., Febvay, G. and Fayard, J.-M. (2004). Assessment of 35-mer amino-modified oligonucleotide based microarray with bacterial samples. Journal of Microbiological Methods (in press). |
| Posters |
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Reymond, N., Charles, H., Beslon, G. and Fayard, J.-M. (2002). ROSO: a software to search optimized oligonucleotide probes for microarrays. ISMB2002: Intelligent Systems for Molecular Biology (Edmonton, Canada) 03-07/08/02. |
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Reymond, N., Charles, H., Beslon, G. and Fayard, J.-M. (2002). ROSO: a software to search optimized oligonucleotide probes for microarrays. JOBIM 2002: Journées Ouvertes Biologie Informatiques et Mathématiques (Saint-Malo, France). 10-12/06/02. |
| JPGD 2002 |
Reymond, N., Charles, H., Beslon, G. and Fayard, J.-M. (2002). ROSO: a software to search optimized oligonucleotide probes for microarrays. JPGD'02: Journées Post-Génomique de la Doua (Villeurbanne, France). 21-22/03/02. |
| Designs |
|
| Organism |
Number of interest genes |
probe size |
Person in charge |
Design results |
| Kluyveromyces lactis |
47 |
50 |
S. Casaregola |
1 probe per gene.
Identical genes: 0.
|
| Ralstonia solanacearum |
5133 |
70 |
C. Boucher |
1 probe per gene.
Identical genes: 15.
Tm range: 7 °C.
Specific probes: 4924 (96 %).
Run 1: 4677 (91 %) optimal probes.
Run 2: 415(8 %) supplementary probes.
Run 3: 22 (1 %) last probes. |
| Homo sapiens |
22322 |
55 |
P. Barbry |
1 or 2 probes per gene.
Identical genes: 1572.
Specific probes: 19875 (92 %). |
| Buchnera aphidicola |
609 |
35 |
BF2I |
2 probes per gene (3 for transport and amino-acids metabolism genes).
Identical genes: 2.
Tm range : 11 °C.
Specific probes: 1272 (98 %).
Run 1: 1087 (86 %) optimal probes.
Run 2: 166 (13 %) supplementary probes.
Run 3: 17 (1 %) last probes. |
NOTE:
Identical genes: any pairs of genes showing more than 98 % identity on more than 100 bases (or 95 % for
EST sequences).
Specific probes: probes with no significant cross-hybridization.
Probes after run 2 and 3: probes with putative secondary structures (more and more stable).
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