Presentation on theme: "MaizeGDB: Four Usage Cases Trent Seigfried 1, Carolyn Lawrence 1, Darwin Campbell 1, Mary Polacco 2, and Volker Brendel 1 1 Iowa State University, Ames,"— Presentation transcript:
MaizeGDB: Four Usage Cases Trent Seigfried 1, Carolyn Lawrence 1, Darwin Campbell 1, Mary Polacco 2, and Volker Brendel 1 1 Iowa State University, Ames, IA 50011, 2 USDA/ARS Abstract: 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.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. Lets 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. Lets explore a few. 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 youre 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 youre 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 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 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 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. Lets 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 D4: The link to the primer itself gives details on its usage, as well as contact information to the submitter if you have additional questions. Figure D5: The probe link for the primer provides detailed information about the probe (an SSR here). You can find the repeat, the 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. 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 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. Other useful MaizeGDB features… Figure E1: A step-by-step tutorial explaining many of the features of MaizeGDB is available on the front page of the site. Figure E2: Educational resources, perfect for incorporating maize into your classroom, are also available from the front page. Figure E3: Need to find a maize researcher? MaizeGDB contains an updated database of addresses, phone numbers, and emails! Figure E4: Each page features a shortcut menu, which will quickly take you to many of the more popular and useful pages in MaizeGDB. Figure E5: Each page also features a search tool, enabling you to quickly search through your data type of choice from anywhere on the site. Figure E6: In addition, youre 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! 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. Whats coming up at MaizeGDB? 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 havent already!http://www.maizegdb.org Fill out the survey or leave us feedback! Wed 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!