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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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. 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.
Click on the view menu, and check editable sequence. Each group should choose one of the sequence files on the disk, and copy it from drive A to the desktop. I first group all the forwards together, then all the reverses.
BioEdit can also edit chromatograms, but I find Chromas to be nicer. This opens the file in Chromas see below under installation notes if some other program opens it instead of Chromas. If this does not occur, repeat the process with the reverse complement sequence file in a New alignment.
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.
Enter that information in the header of the MEGA file. Select both files with the mouse by dragging it over the file names at the left.
Identify the region of vector sequences. Once you set your preferences on one machine you can copy the bioedit. Next go View, Customize Menu Shortcuts. Select the N and replace it by typing in the appropriate base. Look in the Desktop or wherever else you saved the edited sequence ttuorialfiles of type All files.
Sequence editing using BioEdit
I always keep the BioEdit file with all forwards, tuyorial 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. Since this may interfere with analysis of the sequence, these will have to be edited out.
Once I have edited all of my chromatograms I copy the. Move cursor between the top of the selected region and the previous biooedit. The chromatograms come off the machine with all bases in upper case. This file contains the sequence of the multiple cloning site region of pSTBlue Note that this works best with coding sequences without indels as every sequence is an identical length, it is all a bit trickier with tuhorial length sequences.
BioEdit Tutorials – Practical Bioinformatics
Return to your edited forward sequence file, delete the vector sequences, and save for next week. As far as I can tell there is no difference between saving your file as a BioEdit formatted file versus as a fasta file. For each gene within a dataset I usually have this file bioeditt the forward, reverse and consensus. Now place the cursor in the same place in the consensus sequence. Because of this, the bases at the beginning of each sequence file you have tutorixl vector sequence, rather than cloned sequence.
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. Delete and copy the data of highlighted sequence. Hit save control-shift-s and repeat for each group of sequences. Move cursor between the residue and the previous residue. Much editing in BioEdit requires extensive repetitive actions, so using the menus will rather slow. Note how many replacements it does, this is the number of samples.
Note that this is also displayed in a 5′-3′ direction, so the sequence complementary to the beginning of your original unedited forward sequence will be at the end of the reverse complement.
Select them all tugorialcopy to clipboard control-cgo back to BioEdit, to paste these names over the existing ones. At that point I finish my consensus sequence. This highlights any columns that have different bases. Click on File menu, Open.
Guide to editing sequences with Chromas and BioEdit
These should show an almost exact match to the forward or reverse sequence. Select all the reverse sequences and cut them. In BioEdit, clean up all the ends and get things to the base pairs you want to analyze. Paste Sequence s command pastes the sequence title and residues.