Structure Annotation: HOW-TO
( Special thanks to Mr. Michael Lawler of Nevada High School )
PlantGDB is a project at Iowa State University funded by the National Science Foundation. The project involves staff and students in the group of bioinformatics professor Dr. Volker Brendel and seeks to provide resources, tools, and analyses for plant comparative genomics. A key part of our work is to annotate plant genomes and in particular to find all the protein coding genes in the genome. It turns out, YOU can help with this! This site is designed to teach you both the biological background and the step-by-step procedures of gene structure annotation. If you are a high school teacher, this site might provide a module for your classroom. If you are a student, you could begin your studies right here and now - all you will need is provided via web tools. Please contact us with questions and suggestions.
In order to understand what we'll be doing, it is first necessary to understand a few basic concepts and vocabulary terms . Please look through the list of relevant vocabulary terms and visit some of the excellent informational sites also listed on this page.
Simply put, we'll be comparing a sequence of DNA with all previously sequenced strands of DNA and RNA to see if there are any matches, or correlations, and to see how many, if any, genes may be located within the sequence. The reasons for doing this are many fold. The information gleaned from this process can be used a number of ways, all of which will advance our collective understanding of biotechnology and genetics.
Shortly, you will be entering a sequence of DNA from a selected list into a program called "GeneSeqer" ( What is GeneSeqer? ). When you submit this sequence, it will be compared to sequences stored at the national database ( GenBank ) where all previously recorded biological sequences (DNA,RNA,and protein) are stored. What you get back from this submission will be all of the DNA sequences in GenBank that match your sequence along with their description, where they came from, and who worked with them. You can then compare these sequences with your sequence to see which organisms match and possibly what the functions of the matching sequences are. The output is also very helpful in discerning where actual genes may be located on your DNA sequence.
When you feel you are familiar with the vocabulary and are ready to begin, please continue: