Sequence Viewer: Six Frame Translations
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Sequence Viewer: Six Frame Translations

August 28, 2019

In this video I’ll show how to display the six frame translations of an mRNA using Sequence Viewer from NCBI. I’ll start with Sequence Viewer already open to an mRNA. The URL is shown at the bottom of the screen. Right in the middle we see this red bar that represents the protein product of the mRNA. To see the start region better, I’m going to zoom to see the first 450 bases. This is the same red bar, I’m going to click on it to see some guide lines. Next I’m going to click the configure button. Then, click the sequence tab and then turn on the six frame translations. We have options in here that allow us to control the size of the reading frames that are recognized. I’m going to change this so it shows all the possible reading frames. Then click configure to accept our changes and close the dialog. Now we see the tracks shown and if we follow the guidelines, we see the start of the protein lines up with this start codon. The green marks represent start codons and the red marks represent the stop codons. If we look just upstream we see another possible start codon, The decision for the annotation is based on an established body of research about a this gene including a publication that asserts the use of the downstream ATG site. If we look further upstream we see another possible reading frames. If we click and drag all the way to the right, we see that the protein lines up with one reading frame as we’d expect and the end, the end of the protein lines up with the end of the reading frame. This is just one example, there’s a lot more you can do with these tools. Please visit the NCBI website to learn and do more. Thanks.

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