Sequence Research Tools

Click here for access to resources for the B73, Mo17, and Palomero project pages as well as various other sequence projects.

Visit the Maize Genome Sequencing Consortium's Maize Genome Browser! (Find out more about the B73 Maize Sequencing Project here.)

Simple Sequence Search: This search form allows you to just enter basic info (such as accession number, GI number, or a part of the sequence title) to quickly retrieve the desired sequence. Use % as a wild card.

Just as with accession numbers, you can retrieve sequences by GI number (try 12045510) or through the sequence description (try %adh1%, for example).

This search can be executed on every page on the site by utilizing the form in the upper right corner. Choose "sequence" from the drop-down menu, enter your search term in the field, and hit return to find the sequence you're looking for.

MaizeGDB BLAST: The MaizeGDB BLAST tool.
GeneSeqer Gene Discovery Tool: Do a GeneSeqer search.
Mapped Sequence Search: Enter a list of sequence accession numbers and find out if they're mapped and on what maps.

About Clone Ordering: We are attempting to work out arrangements with groups that are making clones available, but many clones are simply unavailable. Please note that MaizeGDB does not ship or store clones, microarrays, library plates, or any other reagents; we merely hope to connect users to these resources when we are aware of their availability.

Details on Contigs

We store membership information for genomic and EST/cDNA contigs built at PlantGDB and for the maize gene index EST tentative consensus (TC) contigs built originally by TIGR and later by the Dana Farber Cancer Institute. If you look up a sequence using its GenBank identifier at MaizeGDB, on the sequence display page you will find links to PlantGDB and TC contigs that include that sequence.

The PlantGDB EST and cDNA assembly pipeline is described here. The PlantGDB GSS assembly is described here. The current version of the PlantGDB contigs is based on GenBank release 157a.

Discussion of Sequence Data for the General Public

What is sequence data?

All living things are described on a basic level by long strands of DNA. These long strands of DNA are composed of nucleotides of four distinct types: adenine (A), cytosine (C), guanine (G), and thymine (T). DNA is merely a long connected string of these four chemicals, often written together as a string of the letters (for example, ACGTGGC).

A sequence, then, is a consecutive listing of these chemicals. Sequence data is usually presented as a long string of capital letters, each representing a specific chemical from the source substance.

What value does studying sequence data have?

Studying sequence data allows us to determine the exact source of each protein within an organism and thus vastly increase our understanding of that organism. Sequence data is the "source" information for probes, loci, and most other types of biological information we might discover.

What is the connection between corn and sequence data?

The sequence data stored here provides information relevant to the study of maize (corn). For instance, we have records (like this one for adh1) that provide detailed information on exactly where a particular element is located in respect to other elements on corn chromosomes; these known sets of distances between loci are called maps. We also provide information on probes, which are genetic tools that are used to specifically locate and describe a particular sequence, as well as loci (plural for locus) which provide information relating the various sequences to one another and indicating the meaning and use of such sequences. By combining all of this data together, we can create a very valid picture of specific pieces of maize and learn how to treat corn diseases, improve corn yields, and make corn more nutritious.

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Last updated 9:00 am, Jan 06, 2009.