Tom Hall. North Carolina State University, Department of Microbiology. This is likely to be the final release of BioEdit. There may be some bugs. BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by a graduate student. BioEdit can also edit chromatograms, but I find Chromas to be nicer. MEGA also has an alignment editor, but I’ve not really used it very much. Double click on the .

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Now when you double click on a chromatogram it will open in Chromas. Select from the next next residue to the end. It is the only program I know of that allows you to edit, search and bioefit, and paste over the sequence title names independent of your sequences. For each gene within a dataset I usually have this file with the forward, reverse and consensus. Not copied to the system clipboard. The reason why I paste them to a new file first is that importing from the clipboard File, Import from Clipboard will place them at the bottom of your file, which is usually not where I want them be.

Click on hutorial view menu, and check editable sequence.

Repeat this process for the pstblue1vector. Now Tutoriial select all the forward sequences and cut them and scroll right to check for any bases changes that need to be checked. These are my preferences, you can use these or change them whatever you prefer.

This changes the way the sequences are displayed.

Sequence editing using BioEdit

If the program sticks the. Then reverse compliment all of them and they should be perfectly aligned relative to the forwards. Raw sequence files will be edited this week, and the edited sequence bioerit will be analyzed next week. Select both files with the mouse by dragging it over the file names at the left. Select a square region.


Sequence editing using BioEdit

All of that probably sounds very confusing, once you have carefully worked through it a couple of times it becomes very easy. Close BioEdit, reopen your files and the settings should all be saved.

Save the file as text only and make sure it has the correct file extension. Just be sure to select to end from a different location each time to reduce the chances of pasting the wrong reverse into your consensus.

On the lower toolbar 3rd of the alignment window, select the first solidly colored button. Actions different from the windows standard are written in red. The most tutprial aspect is that you have to manually align up each sequence and manually create a consensus sequence which commercial programs like Sequencher and Vioedit are very good at. You may have to scroll down the program list to find it. Note that sequences after bases become increasingly unreliable, and are not worth spending much time on.

One quirk of BioEdit is that if you double click a data file it will open in a new copy of BioEdit, not in an existing one.

Guide to editing sequences with Chromas and BioEdit

Change the view type on the lower toolbar 3rd of the alignment windowselect the third colored button from the left says Shade identities and similarities when you hold the mouse over it. It can be helpful to make sure any missing bases are labeled with an n, only use a – for indels so that you can easily distinguish which is which. Paste Sequence s command pastes the sequence title and residues.


I then create a second file which has only the. Click on the view menu for the original unedited fileand check Reverse Complement. My sequence names look tutorila this, PU Since this may interfere with analysis of the sequence, these will have to be edited out. At the end of this phase you have done two data checks, one when you edited your original chromatogram, second when you checked any unique base pair changes.

If the vector sequence given is the opposite strand to the forward sequence, then there should be a region of almost exact homology with the end of the reverse complement. Then I run a NJ analysis to see what is going on with the dataset. Click on the edited forward sequence file to open it.

Click on the File menu, Import. Remove the existing sequences from the tugorial sequence hit control-shift-end, then hit deletethen paste in the ones you just copied.

You can download my bioedit. Make sure your mode is set to edit and insert. Go Edit, Paste Over Titles. These should show an almost exact match to the forward or reverse sequence.