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How to annotate a gene ?

Meeting on Cenibacterium arsenoxidans annotation - 14/04/05. How to annotate a gene ?. Claudine Médigue Atelier de Génomique Comparative. GENOSCOPE/CNRS UMR “Structure et évolution des génomes” Dir. Jean Weissenbach. Select genomes («Option») using the following proposed rules :.

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How to annotate a gene ?

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  1. Meeting on Cenibacterium arsenoxidans annotation - 14/04/05 How to annotate a gene ? Claudine Médigue Atelier de Génomique Comparative GENOSCOPE/CNRS UMR “Structure et évolution des génomes” Dir. Jean Weissenbach

  2. Select genomes («Option») using the following proposed rules : • Genomes with the higher % for CDS in Syntons and/or % BBH Initial choice for synteny results visualized in the maps • Select these genomes in the PkGDB list IF available (reasons explain in the « AGC-annotation-tools » presentation) • Complete your selection with RefSeq genomes, and if necessary, add other distant bacterial genomes (of precise biological interest) • Don’t forget to select, from the PkGDB list, your own genome (paralogs) • Have a look to the synteny results («Explore» functionality) Results ordered by % of CDS in syntons with complete genome in PkGDB Results ordered by % of CDS in syntons with complete bacterial proteome of NCBI RefSeq section

  3. Starting annotation : acces to the annotator editor Clic here Or clic here

  4. Starting annotation : acces to the annotator editor AutoFunc results This automatic information does not need to be change With the help of the Analysis Results section This automatic information can be removed, modified, completed, etc. } This information is given only by the annotator

  5. Pre-defined list for expert annotation GenProtEC product type (M. Riley) GenProtEC classification (M. Riley)

  6. Using analysis results to complete each gene annotation -1-

  7. Expert dnaE gene annotation (definitive annotation) - part 1-

  8. Using analysis results to complete each gene annotation -1-

  9. Visualization of synteny organization

  10. Using analysis results to complete each gene annotation -2- Links to NiceProt

  11. Link to NiceProt (E. coli entry for dnaE)

  12. Expert dnaE gene annotation (definitive annotation) - part 2-

  13. Lien à PubMed

  14. Using analysis results to complete each gene annotation -3- Link to NiceEnyme, COG databank, InterPro

  15. Using analysis results to complete each gene annotation -2- Start codon ?… -> loading Artemis

  16. Start codon modification using Artemis software -1- Start codon for CENAR0439 OK (coding prediction curve + Artemis) ? ? Start codon for CENAR0438 WRONG (coding prediction curve + alignments + overlap in Artemis)

  17. Start codon modification using Artemis software -2- -1- select the CDS CENA0438 -2- press the ‘y’ key (= next start codon) -3- check the new start codon position (looking for the RBS motive) CENAR0438 is selected New possible start position (two ‘y’) Value of the new start position

  18. Start codon modification using Artemis software -3- Other possible start position (three ‘y’) Value of the new start position Which one is correct ?.. Have a look to the alignments :

  19. Annotation of CENAR0438

  20. In the MaGe graphical interface

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