S.Prasanth Kumar, Bioinformatician Computational Genomics Genomics: Application using  GRAMENE   S.Prasanth Kumar, Bioinfo...
GRAMENE Home page
Browsing Type in the  search term  (a clone/feature’s accession number or name) and press search icon. 2: or  Choose  spec...
Search Results Click to view in browser
Genome Browsing Or choose a  Synteny map  to view Or you may  select a chromosome  to browse by clicking on it Examples An...
Synteny Rice Chr. & Rice Clicking on a link on the map will let Open a menu of options. Identifies the rice chromosome you...
Rice Chromosome Chromosome information Click on image to zoom in Click go to view synteny with current chromosome MapView ...
Contig View Use  Jump to Contiview , to select a region by two features.
Viewing Results - Contig View
Chromosome View Identifies which chromosome you are viewing. Clicking on the chromosome will move view to that area Area i...
Overview
Gene Order (Synteny) Detailed Overview
Base Pair View
Genomic Sequence
Gene Splice Site Image
Gene Tree
Exons Information
Protein Information
Retrieving Sequence
Export Sequence as Fasta
EMBL flat file output
Thank You For Your Attention !!!
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Genomics application using gramene

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GRAMENE application genome browser and the different utilities

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Genomics application using gramene

  1. 1. S.Prasanth Kumar, Bioinformatician Computational Genomics Genomics: Application using GRAMENE S.Prasanth Kumar, Bioinformatician S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA www.facebook.com/Prasanth Sivakumar FOLLOW ME ON ACCESS MY RESOURCES IN SLIDESHARE prasanthperceptron CONTACT ME [email_address] (Many Slides are from GRAMENE Tutorial Section)
  2. 2. GRAMENE Home page
  3. 3. Browsing Type in the search term (a clone/feature’s accession number or name) and press search icon. 2: or Choose species from available genomes ( see Slide 7 for Rice).
  4. 4. Search Results Click to view in browser
  5. 5. Genome Browsing Or choose a Synteny map to view Or you may select a chromosome to browse by clicking on it Examples Annotation Info Information on the assembly Click to change species
  6. 6. Synteny Rice Chr. & Rice Clicking on a link on the map will let Open a menu of options. Identifies the rice chromosome you are browsing, which is in the center of the diagram. Click on a maize chromosome and select “center gene list” to show rice synteny to that maize chromosome. Navigation for choosing an alternate chromosome or syntenic species
  7. 7. Rice Chromosome Chromosome information Click on image to zoom in Click go to view synteny with current chromosome MapView shows distribution of features at chromosome scales. Use Jump to ContigView at bottom of page to select a region by two features. You are here Choose another chromosome to view.
  8. 8. Contig View Use Jump to Contiview , to select a region by two features.
  9. 9. Viewing Results - Contig View
  10. 10. Chromosome View Identifies which chromosome you are viewing. Clicking on the chromosome will move view to that area Area in red outlined box on Chromosome is the area you are viewing and is enlarged to fill the overview below. Entire Chromosome is displayed at the top Genomes Menu options
  11. 11. Overview
  12. 12. Gene Order (Synteny) Detailed Overview
  13. 13. Base Pair View
  14. 14. Genomic Sequence
  15. 15. Gene Splice Site Image
  16. 16. Gene Tree
  17. 17. Exons Information
  18. 18. Protein Information
  19. 19. Retrieving Sequence
  20. 20. Export Sequence as Fasta
  21. 21. EMBL flat file output
  22. 22. Thank You For Your Attention !!!

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