3. 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)
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
