Transcript ppt - MaizeGDB Tutorials

MaizeGDB: Four Usage Cases
Abstract:
Trent Seigfried1, Carolyn Lawrence1, Darwin Campbell1, Mary Polacco2, and Volker Brendel1
1Iowa State University, Ames, IA 50011, 2USDA/ARS
MaizeGDB is a central repository for maize information for the maize community, combining hand-curated
information on maize genes with high-throughput data from laboratories to provide an overall view of maize genetics and
genomics with an easy to use interface. We present four distinct cases of using MaizeGDB to answer common questions that
maize researchers may have. These cases demonstrate the ease of use and availability of detailed information at your
fingertips with MaizeGDB, including connections to many other online resources for genetic and genomic information.
MaizeGDB is funded by the USDA/ARS and is publicly available for all to use at http://www.maizegdb.org.
I want to order a stock that expresses a certain phenotype…
I want to find out if my sequence is mapped…
Figure A1: From the front page of MaizeGDB,
click on “phenotype” in the left hand menu to
reach this page. Here, several methods of
searching phenotypes are explained.
Figure A2: You can type in a simple descriptive
name into the simple search box. The more
general the term (i.e., “purple”), the more likely
you are to find results. Let’s try searching for
“purple aleurone” to try it out.
Figure A3: Since the term “purple aleurone” is
an exact match, we are taken immediately to the
record. Here, we have a myriad of data and
options about the purple aleurone phenotype.
Let’s explore a few.
Figure B1: From the front page of MaizeGDB,
click on “blast” in the left hand menu to reach
this page. This tool provides a method of online
sequence comparison, as well as instant
discovery as to whether the matches are mapped.
Figure B2: After pasting a query sequence into
the text box and hitting submit, we get a results
page, including a summary table listing the
matches and how many different map locations
are associated with that matching sequence.
Figure B3: Clicking on a matching sequence
from the summary table in Figure B2, we can
see a detailed alignment, as well as information
on maps and the identified marker; usually, bin
location information is found as well.
Figure A4: Clicking on the “see all 3 images”
link on the purple aleurone record takes you
here, which lets you visually verify that this is
the phenotype you’re looking for. This page also
provides links to the variations that cause this
phenotype.
Figure A5: The purple aleurone record also lists
a large number of stocks with the purple
aleurone phenotype, with the ones in bold
available from the Stock Center. Choosing one
of these gives us this record, which shows details
of the stock, as well as the ability to order the
stock from the Stock Center (on top of the right
hand menu).
Figure A6: Clicking on the “Order this stock”
link pops up a shopping cart, which will save
your stocks of interest until you’re ready to
order. All you have to do to order your stock is
click on the submit order link, fill in your
personal information, and click submit, and your
stock will be on its way!
Figure B4: Clicking on the sequence name takes
you to a detailed sequence page, which provides
a wealth of information about the sequence.
Tools for investigating the sequence at many
other sites are available, as are linkages (as
available) to reagent information, gel patterns,
and much more.
Figure B5: Clicking on one of the maps from
the blast result page takes you to a complete
detailed map record with your locus of interest
highlighted. Loci are color coded for easy
reading, and such relevant detail as mapping
population and which loci are core bin markers
are available at a glance.
Figure B6: Clicking on a locus name from the
blast result page provides a ton of information
about the specific marker and its genomic and
genetic context. Reagent information, map
coordinates, expert researchers on that locus,
references, nearby loci, and much more are all
provided in a single page.
I want to see all genes and other elements found in a particular bin…
I want to find primers to help me detect a particular gene…
Figure C1: MaizeGDB provides a tool that
allows you to browse the maize genome bin by
bin. Clicking on the “genome browser” option
on the left hand menu of the MaizeGDB
homepage will take you to this tool.
Figure C2: This tool contains a complete table
of core bin marker information, including
reagent details and links to more information.
These core bin markers provide the delineation
of the bins, which you can browse here.
Figure C3: Clicking on any region of the
genome in C1 will take you to a page like this,
which summarizes the information available to
you about this region of the genome. Note that
the picture highlights the region for you.
Figure D1: From the front page of MaizeGDB,
click on “locus” in the left hand menu to reach
this page. Here, several methods of searching
loci are explained. Let’s attempt to find “tub1”
using the simple search.
Figure D2: Searching for tub1 quickly takes us
to this record, which provides an abundance of
information about tub1. Of particular interest
are the domain experts, which are the individuals
who have published the most in relation to tub1.
Figure D3: Scrolling down the record brings us
to a section listing primers and enzymes. Four
primers for locating tub1 are listed here, with
links to details on their usage.
Figure C4: A quick click of the mouse takes you
to an index of genes and other markers available
in this genomic region.
Side-by-side
comparisons of this region according to four
high-density maps is also given further down the
page.
Figure C5: Sequences that are found in this
region are also available, along with the option
to download them all as a FASTA file for your
own sequence analysis. The same features are
available for EST contigs which we have
anchored to the region.
Figure C6: Also of interest are the BACs that
have been anchored to the region via
fingerprinting.
These BACs are linked to
additional data within MaizeGDB as well as to
more detailed physical map information at the
University of Arizona.
Figure D4: The link to the primer itself gives Figure D5: The probe link for the primer
details on its usage, as well as contact provides detailed information about the probe
information to the submitter if you have (an SSR here). You can find the repeat, the
additional questions.
forward and reverse primer, BAC information,
mapping information, and much more!
Figure D6: Also of note on the locus record is
the detailed mapping information, which can
provide a context for you as you investigate this
gene further. There are also additional tools
available at the click of a mouse, including
searching other databases for tub1 information as
well as Google searching for more information.
Other useful MaizeGDB features…
What do you want to see at MaizeGDB?
Do you have a success story with using MaizeGDB? Are there features you would be interested in seeing at
the site? Let us know! Trent and Carolyn will both be available throughout the conference to discuss the
site with any interested parties.
What’s coming up at MaizeGDB?
Figure E1: A step-by-step tutorial explaining Figure E2: Educational resources, perfect for Figure E3: Need to find a maize researcher?
many of the features of MaizeGDB is available incorporating maize into your classroom, are MaizeGDB contains an updated database of
on the front page of the site.
also available from the front page.
addresses, phone numbers, and emails!
In our effort to provide useful data to the maize community, we are preparing a searchable public repeat
database which will allow users to quickly find pre-annotated sequence repeats from the maize genome and
align them to a query sequence with the ease of use people have come to expect from MaizeGDB. We are
also developing a networking tool that will help you to quickly find researchers interested in similar topics
as you, providing an easy way to connect with other researchers with similar interests in the maize
community!
Do you want to know more?
• Visit the site at http://www.maizegdb.org and try it out if you haven’t already!
• Fill out the survey or leave us feedback! We’d love to hear from you!
• Visit poster P24 to find out more about how MaizeGDB is reaching out to researchers and students in the
community for learning and to make the database better!
• Many other posters discuss displaying their data at MaizeGDB; check out posters P106 and P110 for
examples!
Figure E4: Each page features a shortcut menu, Figure E5: Each page also features a search
which will quickly take you to many of the more tool, enabling you to quickly search through
popular and useful pages in MaizeGDB.
your data type of choice from anywhere on the
site.
Figure E6: In addition, you’re always just a
click away from more help from MaizeGDB
staff! At the bottom of every page is a feedback
link, providing the help you need quickly!