Genome Workbench: Six Frame Translations
Articles Blog

Genome Workbench: Six Frame Translations

September 29, 2019

In this video I’ll show how to display the six frame translations of an mRNA using Genome Workbench from NCBI. I’ll start with Genome Workbench already open to the search view. You can get Genome Workbench at the URL at the bottom of the screen. I’m going to search the NCBI public databases for the following accession: N M _ 0 0 1 1 8 2 . 4 Once the search has returned, I’m going to add this data to my project. Then, I’m going to open a graphical view. Now, I’m going to turn on the six-frame translations from the content menu in the graphical view. Then, before searching for the open reading frames to show the six frame translations, I’m going to close the project tree view, the task view window and reconfigure my windows so I can see search results side by side with my graphical view. Then in the search view, I’m going to select Open Reading Frame Search from the search tool menu. There are a number of settings we can tune here, I’m going to click the filter icon and uncheck the “show only longest ORFs” checkbox if it’s checked and click ok. Now I have a list of all the reading frames in this mRNA. These views of the data are linked and to show that, if I click on one of the rows in the list, the graphical view changes to show the reading frame. If I look at the six-frame translations track I see green and red marks. The green marks are start codons and the red marks are stop codons. If I choose this reading frame and zoom in we see that the start codon lines up right at the start of the protein product. If I scroll to the left, I see another start codon. The decision for this annotation is based on an established body of research about this gene that asserts the use of this downstream ATG site. If I zoom out, scroll to the right and zoom back in, we see the stop codon right at the end of the protein where we expect it to be. This is just one example looking at the six frame translations and the connections between the views in Genome Workbench. There’s a lot more you can do with these tools, please visit the NCBI website to learn and do more. Thanks!

Leave a Reply

Your email address will not be published. Required fields are marked *