1. Welcome to the combined BLAST and Genome Browser Tutorial

2. Genome browser is a dynamic graphical display of several features identified from rice as well as from maize, sorghum, barley and wheat that were mapped on the rice genome. Some of these features are sequenced genetic markers, ESTs, cDNAs, CDSs, genes, insertion and repeat elements. The browser is another option for investigating the organization of rice and other cereal genomes besides the CMap section of Gramene. The software application was developed by the Ensembl project (www.ensembl.org) and modified by the Gramene project.www.ensembl.org Rice Genome Browser

3. Go to the Gramene navigation bar and click on “Genome browser.” Graphical view of the Rice chromosome and some of the features aligned on it Summary of all the features aligned on a given chromosome. Not all features are displayed by default. Customize views can be generated by each user. Select anywhere on the Chromosome to enter the genome view. (See next slide) Enter a desired chromosome number. Search by entering a clone/feature’s accession number or name.

4. View of Genome Browser Red outlined box on Chromosome is enlarged in Overview below. This is the same in the detail and base pair view that will follow. Right click the mouse button anywhere on the Chromosome to re-center the view in that region. Zoom in/out to a desired level of resolution or designate bp start and stop. Adjust your view by entering coordinates.

5. This view represents the detail view of the red outlined box on desired region of the Chromosome. Hover your computer mouse on a feature to learn more about it. See a feature example in Slide-7. Next view in Genome Browser: Detail view

6. Customize Detail View by modifying default tracks displayed The feature tracks displayed are only a fraction of what is available. To customize the tracks displayed, use the drop down menu under features and select advanced. Hit refresh once you have customized your view. See next slide. The “+” or “-” sign will tell you if the track is expanded or closed. The maize_est track is expanded.

7. Customize tracks on the genome browser You can choose to expand or contract the tracks. Only expanded tracks allow you to use the drop down boxes to link to internally or externally. You can customize the tracks by selecting a color of choice. You can customize the tracks to display by selecting the check boxes Once you have finished you will need to save your results. You will then need to hit refresh on your detail browser view.

8. Next view in Genome Browser: Basepair view Links to the project that contributed the BAC clone sequence Links to the CMap (CMap tutorial available also) Links to the nucleotide database at the National Center for Biotechnology Information (NCBI). Basepair view of a given region along with the features mapped in that region.

9. View of Ensembl Gene Report Describes location on the Rice genome. Select to view detailed info from the Genome Browser. Position on the Original BAC sequence. Select to view detailed info from the Genome Browser. Pop-up menus containing Gene, Transcript, and Peptide informational links. Also provides links that allow you to export data. These links provide detailed information on the corresponding Transcript, Exons and Protein.

10. Next view in Ensembl Gene Report Page Detailed information on the transcript and its structure. Displays the transcript structure. Select to view Ensembl Transcript Report. Select to view Ensembl Protein Report (See Slide 11).

11. View of Ensembl Transcript Report Page Legend with color- coded details of the Transcript. Transcript information with drop-down menus containing Gene, Transcript, and Peptide informational links. Also provides links that allow you to export data. Select to view Ensembl Exon Report. Deduced protein sequence with the corresponding gene sequence

12. View of Ensembl Exon Report Provides more display options. Details of the exon structure

13. View of Ensembl Protein Report Page TIGR protein accession Gramene Peptide ID Links provide detailed information on the corresponding Gene, Transcript and Exons (See Slides 5-10 for more info). TIGR annotation of the protein Sequences from TIGR and Gramene with the best match. Protein Structure with pop-up menu containing the exon and splice site Information. Allows you to export data in various formats. (See Slide 13)

14. Next view in Ensembl Protein Report Page Legend with color- coded details of the Protein Structure from previous view. Protein sequence displaying the boundaries of different exons. More display options

15. Export Data Page Enter the feature id/the sequence range in base pairs to export the sequence related information in various standardized formats.

16. Resulting page from exporting data. An example of the data exported in GenBank format, for an Ensembl gene with features mapping in 20kbp region flanking it.

17. BLAST tool allows you to find the best pairwise sequence match to your query sequence. The best match helps you in finding the detailed information/annotation for your query sequence. BLAST Search

18. BLAST Search Page 3. Enter a nucleotide or protein sequence. The sequences can be copied and pasted into the window. 1. Select desired Program. See Program list below for descriptions. 2. Select desired Database. See Database list below for options. 4. Hit the button to “Run BLAST” search

19. BLAST Results Summary Page Select the link to view the pairwise alignment of the query sequence to the respective BLAST database entry. Select a Sequence to view the corresponding Ensembl Protein Report. Indicates the expected value

20. Select the sequence accession to view detailed information on the corresponding sequence entry with the best match. (Follow the genome browser - Slide 5 ) BLAST Results: Alignment section Pairwise sequence alignment of the query sequence to the respective BLAST database entry. Summary of the alignment scores, expected values and percent identities

21. BLAST databases There are a number of sequence datasets available for Rice, Maize, Sorgum, Wheat and Barley cereals in Gramene BLAST searches.