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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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Figure out how many base pairs are present in BioEdit, go to the last base and select it and look at the number. Now scroll right again and look for any bases that need checking. All of that probably sounds very confusing, once you have carefully worked through it a couple of times it becomes very tutorail. Chromas has the advantage the you can save all of your chromatograms which can subsequently be used in any other programs unlike Sequencher which saves everything in a project file which cannot be opened by anything else.

This opens the file in Chromas see below under installation notes if some other program opens it instead of Chromas.

Make sure your mode is set to edit and insert. Then I run a NJ analysis to see what is going on with the dataset. The most annoying aspect is that you have to manually align up each sequence and manually create a consensus sequence which commercial programs like Sequencher and Geneious are very good at.

Now when you double click on a chromatogram it will open in Chromas. 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. This file contains the sequence of the multiple cloning site region of pSTBlue Glu31 and replace with. Depending on how well your reverse sequences overlap with your forwards, scroll right until they overlap with good sequences.


Click on the sequence file you transferred to open it. I paste these into Microsoft Word and use search and replace to get rid of extra details. 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.

BioEdit Tutorials – Practical Bioinformatics

As far as I can tell there is no difference between saving your file as a BioEdit formatted file versus as a fasta file. To correct the consensus sequence I copy and paste the sequences from a population or individual, group, etc. It helps to also have additional individuals from the same population all next to one another too. If you wish to keep them in the same order as they are in your directory then click on the bottom sequence file first, then click on the top one while holding the shift key.

Behavior of BioEdit ver. 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.

Sequence editing using BioEdit

Click on File menu, Open. Enter that information in the header of the MEGA file. This will allow you to see any base pairs that are different in the clean forwards. Raw sequence files bioedti be edited this week, and the edited sequence files will be analyzed next week. 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.


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

Delete and copy the data of highlighted sequence.

Copy the data of highlighted sequence. Editing and most of the analysis will be done using BioEdit, a freeware sequence analysis program developed by Tom Hall at North Carolina State University. 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.

Now place the cursor in the same place in the consensus sequence. Drag ruler 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. It helps if you edit the sequences to start from the same base prior to importing them, that way if you do multiple sequences they are already mostly aligned.

The sequence present in the original file is the sequence of the newly synthesized strand.

Click on Sequence menu, Pairwise alignmentAlign two sequence allow ends to slide.