Transcript BLAST_and_Genome_Browser_tutorial

Rice Genome Browser
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.
Go to the Gramene navigation bar and click on “Genome browser.”
Search by entering a
clone/feature’s accession
number or name.
Enter a
desired
chromosome
number.
Select anywhere on
the Chromosome to
enter the genome
view.
(See next slide)
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.
View of Genome Browser
Right click the mouse button
anywhere on the
Chromosome to re-center the
view in that region.
Red outlined box on Chromosome is
enlarged in Overview below. This is
the same in the detail and base pair
view that will follow.
Zoom in/out to
a desired level
of resolution or
designate bp
start and stop.
Adjust your view by
entering coordinates.
Next view in Genome Browser: Detail view
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.
Customize Detail View by modifying default tracks
displayed
To customize the
tracks displayed, use
the drop down menu
under features and
select advanced.
The feature tracks
displayed are only a
fraction of what is
available.
The “+” or “-” sign will tell
you if the track is
expanded or closed. The
maize_est track is
expanded.
Hit refresh once you have customized your
view. See next slide.
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.
Next view in Genome Browser: Basepair view
Basepair view
of a given
region along
with the
features
mapped in that
region.
Links to the
nucleotide database
at the National Center
for Biotechnology
Information (NCBI).
Links to the project that
contributed the BAC
clone sequence
Links to the
CMap (CMap
tutorial
available also)
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.
These links provide
detailed information
on the corresponding
Transcript, Exons
and Protein.
Pop-up menus containing Gene, Transcript, and
Peptide informational links. Also provides links
that allow you to export data.
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).
View of Ensembl Transcript Report Page
Select to view Ensembl Exon
Report.
Transcript information with drop-down
menus containing Gene, Transcript, and
Peptide informational links. Also
provides links that allow you to export
data.
Deduced protein sequence
with the corresponding gene
sequence
Legend
with colorcoded
details of
the
Transcript.
View of Ensembl Exon Report
Details of the
exon structure
Provides more display options.
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.
Allows you to export data in various formats.
(See Slide 13)
Protein Structure with pop-up
menu containing the exon and
splice site Information.
Next view in Ensembl Protein Report Page
More display options
Protein sequence
displaying the
boundaries of
different exons.
Legend with colorcoded details of the
Protein Structure
from previous view.
Export Data Page
Enter the feature
id/the sequence
range in base pairs to
export the sequence
related information in
various standardized
formats.
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.
BLAST Search
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 Page
1. Select desired
Program. See Program
list below for descriptions.
2. Select desired
Database. See
Database list below
for options.
3. Enter a nucleotide or
protein sequence. The
sequences can be copied
and pasted into the
window.
4. Hit the button to
“Run BLAST” search
BLAST Results Summary Page
Select a Sequence to view the
corresponding Ensembl Protein
Report.
Select the link to view the
pairwise alignment of the query
sequence to the respective
BLAST database entry.
Indicates the expected value
BLAST Results: Alignment section
Summary of the
alignment scores,
expected values and
percent identities
Select the sequence
accession to view
detailed information
on the
corresponding
sequence entry with
the best match.
(Follow the genome
browser - Slide 5 )
Pairwise sequence
alignment of the
query sequence to
the respective
BLAST database
entry.
BLAST databases
There are a number
of sequence
datasets available
for Rice, Maize,
Sorgum, Wheat
and Barley cereals
in Gramene BLAST
searches.