1. P. sojae P. ramorum P. capsici

2. Detailed manual in use of JGI site

4. Genome Browser Can type or paste text in here Then type return or click “Refresh” Change orientation of sequence Display 3 frame translation (must be zoomed in) Display DNA sequence (must be zoomed in) Sequence similarity to P. ramorum Blue = coding Pink = non-coding EVERYTHING IS CLICKABLE!! Click this to access the DNA sequence Tracks give different versions of gene models as well as various sets of Blast hits Clicking on a track will expand it (see next page) Current “best” gene models

5. Expanded track Red models have been manually annotated Clicking on open models will open the protein page

6. Clicking on model will open the nucleic acid sequence Clicking on green bar will open the protein sequence introns Clicking names will open gene in its database Clicking gray bar will open sequence alignement red blocks are insertions in target Clicking red dot will set sequence as source Protein page EVERYTHING IS CLICKABLE!! Clickable All clickable Blue indicates EST support for UTR

7. Shift click or command-click to choose lists of sequences to get (in fasta format) or do Clustal alignments on Shift click or command-click to choose lists of genomes and/or databases for the list of alignments. Then click “Apply Filter” number of alignments to display Protein page OPTIONS

8. Sequence Display FROM PROTEIN PAGE Padding controls how much flanking sequence is displayed Introns (should start with GTxxG) Blue indicates EST support for UTR

9. Advanced Search (much easier than Simple Search) Shift click or command-click to search mutilple databses simulataneously It’s also an easy way to switch databases Do NOT type return or enter after your entry - you MUST click “Search” Accepts and recognizes almost any kind of query Output of search

10. Links: P -> protein page T -> transcript page G -> genome browser Check to download sequences

11. Transcript page Contains more info on annotation Used mostly for manual annotation

12. Gene Ontology Click to go to protein page

13. KEGG Click to go to protein page