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Accessing Gramene

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(If some website features don't work correctly, try using a different browser) ... John Mullet, Texas A & M. Patricia Klein, Texas A & M. Robert Klein, USDA-ARS ... – PowerPoint PPT presentation

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Title: Accessing Gramene

1
Accessing Gramene

To access Gramene, open your browser (such as
Netscape, IE, Mozilla, or Firefox). (If some
website features dont work correctly, try using
a different browser)
In the address bar type www.gramene.org and press
Enter to open the Gramene Home Page.

2
Home Page Navigation
Only on home page, indicates Gramene release
number being used
Select feedback from any page to reference that
page and open a communication box. Use for asking
questions or giving feedback.
Click on Gramene Logo to return to the Home page
3
Home Page
Quick search, found at the top of all other pages
Gramene Tips give advice on using the site. The
Archive contains all tips.
News about the current release and the grass
genomic community is listed here, along with a
Gramene Calendar.
Quick links help get you directly to where you
want to go
4
Non-home Page Navigation
This heading is on all pages except for the home
page.
Quick search, optionally select a specific
database to search, enter a term to search for,
and click on search.
Title identifies the page being viewed.
Click logo to return to Home page
Dropdown Navigation Bar (see next slides)
Easily accessible Feedback button on every page.
5
Searches
Each module has its own module-specific
navigation bar below the main Gramene navigation
bar.
Module specific searches will search ONLY that
module (the example here is the QTL module
Gramene Modules and tools used to access the
databases. See individual module tutorials.
6
Genomes
Select Genomes to access the genome browser, as
well as search tools GrameneMart and BLAST Logo
to return to the Home page
Select which genome to view. Also available are
Rice-Maize synteny diagrams.
7
Downloads
Download data or software to install Gramene on
your own machine.
8
Resources
Defines terms, abbreviations and acronyms used.
Links to other on-line glossaries
Click to browse fact pages on different grass
species
Provides links to other websites of interest
Submit a gene or ontology term to the database
Links page of genetic newsletters for rice
9
About
Click to access Gramene information and history.
10
Help
Gramene help docs and documentation
Searchable Frequently Asked Questions about
Gramene, curation, and database modules.
E-Lists for discussion and for announcements
Link to info on Rice gene nomenclature
11
Footer
Images link to species information pages
Collaborators and funding sources are linked
along the bottom
Information about citing Gramene
Gramene purpose, history and people
Provides an overview of everything on the site
12
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13
Gramene database - 9 modules
14
Rice Genome
15
Map of Chromosome 11
16
Screenshot of BrowserChromosome 11
17
V. 20
Rice QTL added to next release.
18
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19
Customizing the Detail View
Arrays
Jump To
Features
GSSs
Decorations
Width
Export
FSTs
ESTs
Markers
20
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21
BLAST Home Page
Sequence Information Enter a sequence that you
have and are trying to locate, or are trying to
find a similar sequence for
DNA codes contain ACTG Peptide codes contain
GALMFWKQESPVICYHRNDT
Search Information where would you like to
search for similar sequences, using which tool?
compares a nucleotide (dna) query sequence
against a nucleotide sequence database
compares a nucleotide query sequence translated
in all reading frames against a protein sequence
database
22
Gene Detail PageGeneral Info
Gene name Traditional gene names have been used.
Some gene names have been modified according to
the Gene Nomenclature System. Gene symbol Gene
symbols have been assigned, according to the Gene
Nomenclature System. Gene synonym List of names
or symbols that have been used for a specific
gene. Description Text defines the primary
features used to detect the phenotype and other
related information for a particular gene to
distinguish it from the wild type. Phenotypic
image (if available) Display image(s) and text
explanation of phenotypes for a particular gene.
Click a thumbnail to enlarge image.
23
Literature
Gramenes ID for that reference
Click here to link to cross-referenced resources.
24
Ontology
External references used for defining or
associated to synonyms
Exact ontology term
Definition of the term
The lineage of alpha-amylase activity as a
molecular function
Term-term relationship i IS A (type of)
Number of database objects associated in the
database with this term.
Click on link to get a complete list of set of
genes/proteins/QTL/maps etc. that may be
associated with the given ontology term (see next
slide for oryza sativa example.)
Links to source that originally developed this
ontology.
25
General Protein Info
Proteins
Shows the name(s) of the protein molecule based
on its function or phenotype
Alternate names used in various databases and
scientific literature.
Click for BLASTP query to find best match(es) to
peptide sequences deduced from the TIGR rice gene
models.
Cross references to GenBank and SWISSPROT protein
entries.
Species and cultivar (stock) from which the gene
was sequenced
A textual description of the protein
26
Protein Detail Page Similarities
Click these options to link to NCBIs BLink to
display the graphical output of pre-computed
BLASTP results against the non-redundant (nr)
protein database from NCBI.
Click these options to find if there are any
known proteins that share the structural homology
with the given protein
27
Ontologies

An Ontology is a common vocabulary used to
facilitate communication between researchers and
databases.
An ontology matches classification and reasoning
methods of the computer.
Ontologies can be indexed objectively by a
computer.

28
Ontologies at Gramene

Plant Ontology
Plant Structure(PO)
Growth stages (GRO)
Gene Ontology (GO)
Molecular Function
Biological Process
Cellular Component
Environment Ontology (EO)
Gramene Taxonomy (Gr_tax)
Trait Ontology (TO)

29
Map Types

genetic maps - indirect estimate of the distance
and order of the sequence use markers provide
framework for genome sequencing.
physical maps- estimate of the true distance
(base pairs) define sequence between markers
used for gene identification.

30
Features

Everything that can be mapped
Gene sequence of DNA that codes for a product
that in turn has a predicted or demonstrated
impact on phenotype.
(Some genes not yet associated with sequences)

31
Molecular Markers

Molecular markers are the genetic signposts (dna
segments) that flag the presence of genes that
control particular traits. Once we know about a
useful molecular marker, plant breeders can test
the seeds or leaves of a plant to make sure it
has the allele they are looking for.
Molecular markers can be generated by a variety
of different techniques, and information
surrounding these markers will vary quite a bit
depending on the marker type.
When we know what alleles a plant has at loci
associated with critical traits of agronomic
importance and what those alleles do. We can make
predictions about whether it can thrive in
certain conditions.
Measuring such characteristics by conventional
methods is much more difficult, time-consuming,
or expensive, since it requires the organism to
grow to maturity.

32
Gramene Markers
33
Markers Screenshot
34
QTL

A QTL (or quantitative trait locus) refers to a
particular region of DNA that is hypothetically
associated with a particular trait.
Based on the idea that some traits are controlled
by multiple genes.

35
QTL Screenshot
36
Overview of concepts in Gramene
37
Mapped Features
38
Help