DNA Subway (www.dnasubway.org)

The first educational product released by iPlant, DNA Subway (www.dnasubway.org) presents complex scientific tools and data in an intuitive and appealing interface, and makes high-level genome analysis broadly available to students and educators. "Riding"

DNA Subway is a discovery environment to analyze DNA using bioinformatics. It puts all the tools and data into one place, eliminating guesswork as to what is needed, when and where. Using the Red Line, you can predict and annotate genes in up to one hundred thousand base pairs of DNA. Using the Yellow Line, you can prospect entire genomes for similarity to specific sequences. Additional lines are being developed to analyze EST data and to work with phylogenetic trees. You can use DNA Subway as a guest user, however, only registered users can save and share their work. To begin a project, click a square. DNA Subway includes sample data from a number of different organisms with which you can work. You can also upload and analyze your own data. Label the sequence with this information. To speed up this process, you first mask repetitive DNA. Then, you can identify evidence for genes by using gene prediction programs and database searches. You can search the databases UniGene and UniProt, which contain known genes or proteins. Or, upload and search your own data. A "v" in front of a button indicates that you can view the results of that analysis. When you click on the repeat/masker button after the process is completed, you can get a table showing the region where your repeat appears, as well as the type of repeat detected. Use the Apollo sequence annotation tool to build gene models from your gene evidence, and upload these models back into the Red Line. View your DNA in a local browser. Browsers use boxes and lines to represent exons and introns, and allow you to zoom in and out of your DNA sequence. If you work with one of the sample sequences, you can also export data to a genome hub such as Phytozome. There, view your results alongside the results other scientists have found and published for the sequence. Finally, you can transfer a gene to another line to extend your analysis. Use the Yellow Line to search a number of genomes with the DNA or protein sequence as query. You can display matches as multiple alignments or group them by degree of similarity in a tree view.

DNA subway, bioinformatics, iPlant

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