P. sojaeP. ramorumP. capsici

Detailed manual in use of JGI site

Tutorial in use of JGI site- includes guide to structural and functional annotation

(not enabled in P. sojae and P. ramorum databases but info is generally useful)

Genome BrowserCan type or paste text in hereThen 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. ramorumBlue = codingPink = 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

Expanded track

Red models have been manually annotated

Clicking on open models will open the protein page

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 pageEVERYTHING IS

CLICKABLE!!

Clickable

All clickable

Blue indicates EST support for UTR

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 pageOPTIONS

Sequence DisplayFROM PROTEIN PAGE

Padding controls how much flanking sequence is displayed

Introns (should start with GTxxG)

Blue indicates EST support for UTR

Advanced Search (much easier than Simple Search)

Shift click or command-click to search mutilple databses simulataneously

It’s also an easy way toswitch 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

Links:P -> protein pageT -> transcript pageG -> genome browser

Check to download sequences

Transcript page

Contains more info on annotation

Used mostly for manual annotation

Gene Ontology

Click to go to protein page

KEGG

Click to go to protein page