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. I manually align them and check for obvious missing bases and either correct them or add a gap to preserve the alignment. 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.
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Then reverse compliment all of them and they should be perfectly aligned relative to the forwards. Tuyorial and replace with. Eventually the forwards will start to be a poor match to the reverses.
If the program sticks the.
Figure out how many base pairs are present in BioEdit, go to the last base and select it and look at the number. 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.
Select them all control-acopy to clipboard control-cgo back to BioEdit, to paste these names over the existing ones. 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. This highlights any columns that have different bases.
As far as I can tell there is no difference between saving your file as a BioEdit formatted file versus as a fasta file.
Note that I have changed or set many menu short cuts see BioEdit stuff to bioediit after installation below to make things quicker, thus these instructions are based on these changes.
Double click on the chromatogram file usually has the extension ab1. 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.
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 you wish to keep them in the same order as they are in your directory then click on the bottom sequence futorial first, then click yutorial the top one while holding the shift key.
Go Edit, Paste Over Titles.
BioEdit Tutorials - Practical Bioinformatics
I first group all the forwards together, then all the reverses. Much editing in BioEdit requires extensive repetitive actions, so using the menus will rather slow. 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. Now when you double ttuorial on a chromatogram it will open in Chromas.
When you first install BioEdit and Chromas, the default will be that BioEdit opens the chromatogram files. 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. This will allow you to see any base pairs that are different in the clean forwards.
Now I select all the forward sequences and cut them and scroll right to check for any bases changes that need to be checked. Next go View, Customize Menu Shortcuts. Hit control-e to select to the end, hit delete, move right one base then paste control-c.
I paste these into Microsoft Word and use search and replace to get rid of extra details. The regular copy and paste features work between copies of the program, but copying and pasting sequences does not. Create a new BioEdit file. 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.
It helps to also have additional individuals from the same population all next to one another too. Depending on how well your reverse sequences overlap with your forwards, scroll right until they overlap with good sequences. I manually align them and check for obvious missing bases and either correct them or add a gap to preserve the alignment. Enter that information in the header of the MEGA file.
Guide to editing sequences with Chromas and BioEdit
Make sure your mode is set to edit and insert. Go back to your BioEdit file with all your sequences which should still have the original sequences highlightedpaste the sequences control-sthen delete the selected sequences control-dthus replacing the newly edited ones and removing the originals.
To change settings first create a new alignment File, New Alignment or open an existing file.