PBIL

ROSO
a friend for your design

BBE contribution to PBIL in Lyon, France

ROSO a friend for your design

Home sweet home Who did it ?... I did it !:) Principles Try it and you will love it !
Just run it Credentials Comments I help you if I can. You're feeling down.

Articles
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
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
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.
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).

  • INRALaboratory of Functional Biology, Insects and Interactions
    Copyright ROSO 2004
    INSA Lyon