Here is a brief reference to using BioEdit, a multiple sequence editor for Windows. It has many functionalities an is quite comprehensive. The following guidebook was made for a workshop I gave with the CECRI student association at the CHUL hospital / Laval University.

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Subject: BioEdit: sequence alignment editor tutorial

Web address to download this free software: www.mbio.ncsu.edu/BioEdit/bioedit.html

BioEdit Shortcuts Ctrl + N -> new alignment window Ctrl + O -> open saved alignment Ctrl + A -> select all sequences Ctrl + Del -> delete selected sequence(s) Shift + Ctrl + R -> reverse complement selected sequence(s) Ctrl + F8 -> copy selected sequence(s) Ctrl + F9 -> paste selected sequence(s)

Other Useful Shortcuts Ctrl + C -> copy Ctrl + V -> paste Ctrl + F -> find Ctrl + H -> find and replace Shift + selection -> select inclusively Ctrl + selection -> select specifically Ctrl + Z -> Undo Ctrl + Y -> Redo

*to create custom shortcuts, go to [View -> Customize Menu Shorcuts]
“[…]” = menu selections

Importing/Exporting
Importing Sequences from another program/window:
(N.B. should be simple sequence(s) or BioEdit compatible sequence formats like fasta or clustal)
1- Select/Open a BioEdit alignment window
2- Select sequence(s) to import with mouse from other program/window
3- [File -> Import from clipboard]

Exporting a graphical view of an alignment
1- Select sequence titles of interest
2- [File -> Graphic View]
3- Select options then click “redraw”
4- [File -> Export as Rich text ]
5- Select location, add the “.rtf” extension to the file name and save
*N.B. You must save the alignment as a new file, overwriting an older file will not function
6- Open with Word or OpenOffice

Editing Sequences/Alignments
Add a new (blank) sequence to an alignment
1- Select/Open a BioEdit alignment window
2- [Sequence -> New sequence]
3- Enter the Title, sequence type, and sequence into the box
4- Click “Apply and Close”

How to edit sequences
1-Double click on the Title of the sequence in alignment window
or
1- Click on the “lock” icon twice (top left in alignment window)
2- Choose the “edit” mode (above lock icon)
3- Select “overwrite” or “insert”
4- Click on the desired sequence and type in modifications

Find a subsequence or a motif
1- Select sequences
2- CTRL + F
-or [Edit -> Search -> Search for User-defined motif]
*N.B. user-defined allows to search for ambiguous characters (i.e. “N”, “R”, ...)

Removing Gaps or spaces
1- Double click on the “lock” icon
2- CTRL + SPACE

Reversing sequence order
[Sequence -> Manipulations -> Reverse]

Complement sequence
[Sequence -> Nucleic Acid -> Complement]

Translate Nucelic Acid sequences to Protein
1- Select sequence title or sequence region
2- [Sequence -> Nucleic Acid -> Translate]
OR
[Sequence -> Toggle Translation]

UnTranslate Protein sequence to DNA. (*prediction based on most frequent codons)
1- Select sequence title or sequence region
2- [Sequence -> Toggle Translation]
OR
[Sequence -> Translate or Reverse-Translate]

Multiple Sequence Alignments
Align 2 sequences:
1- Select both sequences to align
2- [Sequence -> Pairwise alignment ]
3- Choose global (fixed ends) or local (ends slide) alignment

How to rearrange sequences
1- Click on the “lock” icon twice (top left in alignment window)
2- Choose the “grab and drag” or “select and slide” mode (above lock icon)
3- Choose the appropriate editing mode, either the icons or [Sequences  Edit Mode]
4- Click and drag

Create a CLUSTALW multiple alignment
1- Remove gaps if you do not want to consider them (usually the case) Ctrl+SPACE
2- Select sequences you wish to align
3- [Accessory Application -> ClustalW Multiple Alignment]
4- Click “Run ClustalW”

Create a Consensus sequence (from alignment)
1- [Options -> Preferences]
2- Select “General” tab
3- Select any characters you want included in consensus from the “Don’t include” column to the “include” column
4- Select “Consensus” tab to choose options
5- Click “Save and close” button
6- [Alignment -> Create consensus sequence]

Restriction Enzyme Maps
1-Select desired sequence
2- [Sequence -> Nucleic Acid -> Restriction map]
3- Choose options then click “Generate map”

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