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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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Overwrite the sequence title onto the next title shifting up, when the title is being edited. If the vector sequence is on the same strand as the forward sequence, the vector should have a region of exact or almost exact homology with the beginning of the forward sequence.

Sequence editing using BioEdit

You can download my bioedit. Indication of selected region on the aligment window not changed. Look in the Desktop or wherever else you saved the edited sequence filesfiles of type All files. Click on the sequence file you transferred to open it. I hate menus, so biioedit that I can use the keyboard for Biosdit tend to change it. This highlights any columns that have different bases.

Select them all control-acopy to clipboard control-cgo back to BioEdit, to paste these names over the existing ones. Not copied to the system clipboard. Each line in the trace is colour-coded to match the colour that one of the 4 bases is displayed in. Save the edited file to the desktop, or preferably, your own disk or network account.

Each group should tutofial on to a PC using the class ID bisc and the password pseud. Once you set your preferences on one machine you can copy the bioedit.


Select to the end including the current residue. Adjust the size of tutoriall chromatogram trace with the Horizontal scale and Vertical scale bars to the top left of the image. On the middle toolbar 2nd in the alignment window change mode to edit, change box next to it to insert.

Guide to editing sequences with Chromas and BioEdit

In that case I try and tutkrial them close, but each individual one many require adjustment. I select a point in the reverse, then select sequence to the end Edit, Select to End, control-e. It helps to also have additional individuals from the same population all next to one another too. Then I run a NJ analysis to see what is going on with the dataset.

Note that I have changed or set many menu short cuts see BioEdit stuff to change after installation below to make things quicker, thus these instructions are based on these changes. Now place the cursor in the same place in the consensus sequence.


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. Glu31 and replace with.

Guide to editing sequences with Chromas and BioEdit

This creates a duplicate sequence that can be edited without changing the original sequence. Click on StartPrograms, and Bioedit. 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. Save the file as text only and make sure it has the correct file extension.


I copy all the forwards to a new BioEdit file, select the sequence titles Edit, Select All Sequences, control-shift-a and copy them to clipboard Edit, Copy Sequences, control-amake the new BioEdit file active and paste them in Edit, Paste Sequences, control-s.

I paste these into Microsoft Word and use search and replace to get rid of extra details. Click on the File menu, New alignment.

Drag ruler with the mouse left button on. You may have to scroll down the program list to find it. Click on Sequence menu, Pairwise alignmentAlign two sequence allow ends to slide.

Before trying to merge the forwards and reverses together, reverse the first reverse sequence Sequence, Nucleic Acid, Reverse Compliment or control-shift-r and align it to your forward sequence usually I have to delete a few bases. I always keep the BioEdit file with all forwards, reverses and consensus sequences so that if I double check stuff later it is easier to find the relevant chromatograms I can tell what sequence is from where by the sequence name.

Repeat this process for the pstblue1vector. On the lower toolbar 3rd of the alignment window, select the first solidly colored button. Next go View, Customize Menu Shortcuts.

To fix this, right click on a chromatogram, select properties, it should say opens with Bioeditt, hit change, browse to the Chromas executable, select it, choose always open with this program, hit ok.