In this tutorial, we’ll learn the basics of navigating the DNA analysis suite and editing sequences. Click here to download a file for the sequence pBR322 to your computer.
View and Edit Sequences
When you open up a plasmid, you will view it in a split workspace with the “Sequence Map” on the left, and the “Plasmid” map on the right.
Use Annotations to Navigate
Click on the various annotations of the plasmid map on the right to automatically jump to those locations on the sequence map on the left
Click on the gear symbol on the upper right corner to toggle on and off different features of the plasmid map.
You can also drag the tabs of the plasmid map around in an order that you prefer.
ORFs and DNA Search
Check the “ORFs” box to view the open reading frames on the plasmid map, and click the wrench icon to customize the ORF settings.
Highlight sections of DNA, and view information (Tm, GC %, length, etc.) on the highlighted section on the status bar on the bottom.
To search for a particular sequence, “ATATAT,” use cmd/ctrl + f, and enter the sequence into the search box.
- Edit the number of mismatches in the mismatches box to “2” so that the search results will include all sequences that include “ATATAT” with up to two mismatches. You’ll see that the search results jump from 1 result to 98 results.You can also use “N” to represent a degenerate base in the search box .
- Use cmd/ctrl + g to go to a specific baseUse cmd/ctrl + f and type in :30:37 to select regions of bases.
View and Analyze Translations
To view translations, highlight a section of the plasmid on the left side sequence map, and right-click. Click “Create Translation,” and then “Forward,” to view the forward translation for that selection.
To analyze the translation, right-click, “Analyze as Translation,” and then you will see the amino acid frequencies, along with other information on the translated region.
To find the reverse complement of a selected section, right-click, “Copy Special,” “Reverse Complement”.
To view the sequence map as a single strand, click the gear icon on the top right of the sequence map (not the plasmid map), and check off “Complement.”
Toggle on or off the split workspace by clicking “Split Workspace” on the bottom right corner.
Change the topology of the plasmid from circular to linear by clicking the “Information” button on the right side panel, and then changing “Topology” from “Circular” to “Linear,” and click “Update Information”.
Learn how to export sequences in this article here.