GRAMENE application genome browser and the different utilities

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. GRAMENE Home page

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. Search Results Click to view in browser

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. 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. 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. Contig View Use Jump to Contiview , to select a region by two features.

9. Viewing Results - Contig View

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. Overview

12. Gene Order (Synteny) Detailed Overview

13. Base Pair View

14. Genomic Sequence

15. Gene Splice Site Image

16. Gene Tree

17. Exons Information

18. Protein Information

19. Retrieving Sequence

20. Export Sequence as Fasta

21. EMBL flat file output

22. Thank You For Your Attention !!!