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MaizeGDB Site Overview & Tour

Overview
Finding Your Way Around
Noteworthy Features
Noteworthy Tools
Using the Database: A Few Examples


Overview

The primary goal of this website is to integrate together data sets from various maize-related projects into an online workbench for the maize researcher. Beyond this, we also hope to provide resources for educators and members of the general public interested in maize research.

Thus far, we have built data structures for data from the Maize Gene Discovery Project as well as for data from MaizeDB. We have recent data sets from both of these databases included in our database and, in the long term, plan to become the primary providers of this data. In the future, we plan to include data from the sequencing projects at Danforth and Rutgers, as well as data from other projects and databases, such as GRIN (Germplasm Resource Information Network).


Finding Your Way Around

Our goal is to lay out the site as intuitively as possible. The overall design was inspired by a variety of websites both biological and of general interest, such as the persistent, clear, and easy-to-find menu and search fields from the pages at TAIR, Barnes & Noble, and AltaVista (among many others); the search results at Google; and the "useful pages" menus on the front page of ZmDB. Thus, every page on the site has a common layout with some features in common, such as a search form and a useful pages menu in the upper right of every page, and the logo in the upper left of every page also serves as a link back home. Let's take a look at some of these pages.

Data Centers (these can always be reached from the "useful pages" menu on the upper right corner every page or on the browse data page):
BACs (bacterial artificial chromosomes)
ESTs
Gene Products
Loci/Locus (including genes)
Maps
Metabolic Pathways
Overgos
People/Organizations
Phenotypes
Probes
QTL Experiments & Traits
References
Sequences
SSRs
Stocks
Variations

Tools (these are just some examples; a complete list of tools can always be found by clicking "tools" on the upper right of any page):
MaizeGDB BLAST Search: Execute a BLAST search against the ZmDB (Maize Gene Discovery Project) sequence data set. This BLAST will also find related map locations!
GeneSeqer Gene Discovery Tool: Do a GeneSeqer search.
PlantGDB BLAST Search: Execute a BLAST search against the PlantGDB data set.
GenBank BLAST Search: Execute a BLAST search against GenBank.
Mapped Sequence Search: Enter a list of sequence accession numbers and find out if they're mapped and on what maps.
Image Browser: Browse through our images to get a visual idea of some of the things that are stored.
Bin Viewer: Browse through the maize genome!


Noteworthy Features

Our website is designed from the ground up to be as useful and easy to navigate as possible for the widest range of people. Some of the features we've included are described below.

HTML standardization: In the bottom right corner of each page, you will see a logo that says "HTML 4.01." This is because our website is striving to comply with the World Wide Web Consortium (W3C) HTML standards. This standard was specified in 1997 and all modern browsers subscribe to this standard. By using this standard, we can be sure that visitors to our site will have little or no problem using the web pages presented here.

The drawback with using this standard is that some older browsers that don't comply with this open standard (or instead try to use their own standard) may have some flaws in rendering some of the pages. To remedy this situation, we recommend an upgrade to Mozilla (the open-source successor to Netscape 4) or Microsoft Internet Explorer version 5 or above. Both of these browsers adhere very strongly to the W3C standards and are becoming the standard web browsing tools.

US Section 508: Also, you will notice a button in the lower right that says "508." We display this button because our pages are designed to comply with Section 508 of the Rehabilitation Act Amendments of 1998. This statute requires that web sites funded by public money should strive to write standardized HTML (see above) with a number of extra specifications, enabling special programs to provide web browsing capabilities to the handicapped.

Search Field On All Pages: In the upper right corner of every page is a search field that enables you to quickly find records in our data. Simply by typing in the name of a gene, an accession number, a phenotype, or other term that you might be interested in, you can retrieve a list of matching results from any page in the database.

"Useful Pages" Menu: Also in the upper right menu of each page is a drop-down list that says "Useful Pages." Choosing an option from this list at any time redirects you to other resources on the site. This allows you to quickly return to major index pages on the site with just a click.

Easily-Downloadable Data Sets: We're attempting to display our data in ways that make it easy for people to download data for their own use. For example, if you look at our genetic map, you can select the table of map coordinates with your mouse and copy and paste this data directly into Microsoft Excel or other popular spreadsheets. From there, you can sort, manipulate, store, and save it in whatever way you would like. This feature is used throughout the site in areas where table-based information displays might be downloaded.


Noteworthy Tools

We're also seeking to include a variety of tools that enable the retrieval of specific data sets.

blast: Our blast tool lets you compare your sequence to the others stored in our database (and some that haven't yet been included, as our blast updates are rather frequent). This tool is integrated throughout the database, allowing you to blast sequences of all types that you find while searching.

Mapped Sequence Accession Locator: Got some accession numbers and want to see if they've been mapped? Just drop them into this tool and you can quickly find the maps they've been mapped on.

You can also find tools such as a chromosome viewer, PlantGDB and NCBI blast, GeneSeqer gene discovery tool, and others. These can be found integrated throughout the site, as well as from the front page and the tools page.


Using The Database: A Few Examples

Below are some of the research questions that have already been asked of our group concerning the database. These questions provide a good review of some of the tools and options our database provides.

How could I find out if the bz2 gene is mapped onto chromosome 1?
You can quickly find out where particular genes are mapped by visiting the locus page and using the search form there (or choosing "loci" on the search menu list in the upper right). Type "bz2" in the field there, and you'll get directed to the bz2 record. A short way into the record is a section entitled "Map Coordinates," which contains a list of all maps on which this gene is found. The maps are named so that the chromosome number is found at the end of the name (i.e., Genetic 1 is the genetic map of chromosome 1).

I have a very short sequence that I suspect of being a mini-exon. What can I find out about this snippet?
Let's say this snippet is the sequence CTACGTAGTACAGG, for example. One obvious place to check is our MaizeGDB blast. However, for such a short sequence, the program doesn't really return good results.

A better place to search is in our overgo data, using our overgo sequence search. Type your sequence into the overgo sequence search and click "submit," and you'll retrieve a list of results (here's the result for CTACGTAGTACAGG). This tool compares both forward and reverse alignment of the collection of overgos we have in our database, and returns the matches with the matching piece highlighted in boldened red.

From there, you can visit the resulting overgo records, find out if these have already found sequence matches that we've stored in our database, or blast the complete overgo yourself.

I have a handful of sequence accession numbers and I want to see if they are mapped.
Got the sequence accessions ready? Then visit our mapped sequence accession locator and paste your accessions into the field. The tool handles up to fifty accessions at once, in either a comma-delimited, space-delimited, semicolon-delimited, or delineated list.


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Last updated 1:43 pm, Dec 03, 2014.

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