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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Copy the data of highlighted sequence. Ttutorial use this feature on nearly every dataset I create. Be careful to copy. 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.

I first group all the forwards together, then all the reverses. On the lower toolbar 3rd of the alignment window, select the first solidly colored button. Hit control-e to select to the end, hit delete, move right one base then paste control-c.

Drag residues with the mouse left button on. Each line in the trace is colour-coded to match the colour that one of the 4 bases is displayed in.

Look in Desktopfiles of type All files. Repeat for each consensus. Once you set your preferences on one machine you can copy the bioedt. This file contains the sequence of the multiple cloning site region of pSTBlue Click on the sequence file you transferred to open it.

There is no auto save function. To get the sequence of the original template strand, the Reverse Complement must be prepared.

Guide to editing sequences with Chromas and BioEdit

BioEdit lets you modify just about anything that it does relative to menus and keyboard short cuts as well as the default settings for displaying data. Click on the edited forward sequence file to open it. Select all the reverse sequences and cut them. Overwrite the sequence title onto the next title shifting up, bioedig the title is being edited. Drag ruler with the tutodial left button on. Remove the existing sequences from the first sequence hit control-shift-end, then hit deletethen paste in the ones you just copied.


Now when you double click on a chromatogram it will open in Chromas. Click on File menu, Open.

Click on the view menu for the original unedited fileand check Reverse Tutirial. Changing mode from others, the cursor moves one residue before. Click on the File menu, Export as text. Adjust the size of the chromatogram trace with the Horizontal scale and Vertical scale bars to the top left of the image.

One trick I find useful later is to always edit your sequences from the same starting base unless the starts are all messyas it makes sequence alignment much easier later. Double click on the chromatogram file usually has the extension ab1.

Select the N and replace it by typing in the appropriate base.

Sequence editing using BioEdit

Figure out how many base pairs are present in BioEdit, go to the last base and select it and look at the number. Next go View, Customize Menu Shortcuts. Actions different from the windows standard are written in red. 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. Select both files with the mouse by dragging it over the file names at the left.


Guide to editing sequences with Chromas and BioEdit

At that point I finish my consensus sequence. Note that this works best with coding sequences without indels as every sequence is an identical length, it is all a bit trickier with different length sequences. Then I undo the cut, select all the sequences Edit, Select All Sequences, control-shift-acopy them control-a–note that copy and pasting sequences is different tutoria any other copy and paste action. It helps if you edit the sequences to start from the same base prior to importing them, that way if you biledit multiple sequences they are already mostly aligned.

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.

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. Save the file as text only and make sure it has the correct file extension.

Select all residues of all the sequences. Select them all control-acopy to clipboard control-cgo back to BioEdit, to paste these names over the existing ones. 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.

If I loose my sequence alignment, at least all my chromatograms with the correct edits are still there to rebuild it from.