BSEdit Online Manual
New Alignment: Create an empty new alignment. Select DNA sequence alignment or protein sequence alignment
in followed dialogs. Shortcut keys Ctrl + N.
Open Alignment: Open an existing MSA file in the local disk. The supported file formats include clustalW, MSF of GCG package, Mega, PIR, Nexus, GDE, Phylip, Fasta and BSEdit project file format. Shortcut keys Ctrl + O.
Simulate Alignment: Create an alignment of random DNA or protein sequences. The length, size and sequence similarity of the alignment can be selected in followed dialog.
Recent File List, Clear All Recent File List:: Stores the recent openned files list and clear the list respectively. The default file number stored is 10.
Exit: Exit the application. Close all open windows. Shortcut keys Alt + F4.
Combine Fasta Sequence: Combine single fasta format sequence files into one file, which can be inputed into BSEdit or as input file for ClustalW etc.
Subtract Sequence: Subtract sequence file. The input file format is Fasta.
Reverse DNA Sequence: Reverse and complement a DNA sequence. The input file format is Fasta.
Retrieve Sequence by Accession No.: Retrieve DNA or protein sequence from the GenBank by Accession Number in Batch.
New: Create an empty new alignment. In DNA/RNA sequence alignment view, it is a new DNA sequence alignment. In protein sequence alignment, it is a new protein alignment. Shortcut keys Ctrl + N.
Open: Open an existing nucleotide or protein MSA file in the local disk. The supported file formats include clustalW, MSF of GCG package, Mega, PIR, Nexus, GDE, Phylip, Fasta and BSEdit project file format. Shortcut keys Ctrl + O.
Save: Saves the alignment in the current file which name appears in the Status Bar of the view. Shortcut keys is Ctrl + S.
Save As: Saves the alignment under a name and format chosed in the followed dialog.
Save All Sequence Respectively: Saves all sequences as a fasta file in a specific directory provided by followed dialog.
Append Alignment: Append an alignment to the current alignment.
Extract Alignment by Region: Extracts a sub alignment based on the specificed start and end position.
Extract Alignment by Position: Extracts all spcified positions as an alignment.
Extract SNP as Alignment: Extracts all variation sites as an alignment.
Reverse and Complement: Reverse and complement all sequences in the alignment, update the view.
Calculate Alignment Complexity: Calculates the complexity of all sequences according to Minosse et al method, by first calculating the Shannon entropy using the formula S = -∑i(pilnpi), where pi is the frequency of each sequence in the viral quasi species. Then, the normalized entropy, Sn, was calculated using the formula Sn = S/lnN, where N is the total number of sequences analyzed (1).
1. Minosse, C., S. Calcaterra, et al. (2006). "Possible compartmentalization of hepatitis C viral replication in the genital tract of HIV-1-coinfected women." J Infect Dis 194(11): 1529-36.
Export Consensus Sequence: Calculates the full length or regional consensus of specified sequences and exports to a specified directory. The sequences for generate consensus can be specified in followed dialog. The index file option of the dialog is for providing position information for the calculation.
Adjust Circular Genome Alignment: Circular genomes sometimes use different positions as the #1 start position due to various reasons. This method uses the start and end position of an index sequence as standard, moves all sequence before the start position to the end, and moves all sequences after the end position to the front.
Type of Alignment (DNA/RNA Alignment View): Converts DNA sequence alignment to RNA sequence alignment, or vise visa.
- DNA: The aligned are DNA sequences. If aligned are RNA sequnences, converts to DNA sequences.
- RNA: The aligned are RNA sequences. If aligned are DNA sequnences, converts to RNA sequences.
Recent File List: Lists all the recently openned files. The defualt file number to be listed is 10. However it can be changed in "View" -> "View Options".
Clear Recent Files: Clears the recent file list.
Close Alignment: Closes the alignment. Shortcut Keys is Alt + F4.
Exit: Exit the application. All openned windows will be closed.
Edit Mode: Selects Edit Mode which includes "Single Sequence" mode and "Whole Alignment" mode.
- Single Item: If checked, current Edit Mode is "Single Item" Mode, if not checked, changes to this mode. Under this mode, editing will only affect current sequence where cursor resides.
- Whole Alignment: If checked, current Edit Mode is "Whole Alignment" Mode, if not checked, changes to this mode. Under this mode, editing will affect all aligned sequences.
- On: If checked, the Insert Mode is On. Under this mode, all input will be looked as insert.
- Off: If checked, the Insert Mode is Off. Under this mode, all input will be looked as editing the current nucleotide or amino acid.
Deselect Selected Region: Deselected the selected region. All menus and buttons related with the selected region will be disabled. Shortcut Keys is Ctrl + X.
Cross Line Selected Region: Cross line all sequences in the selected region.
Under Line Selected Region: Under line all sequences in the selected region.
Mask Selected Region: Masks all sequences in the selected region with "x".
Row Box Selected Region: Marks all sequences in the selected region with horizontal box.
Column Box Selected Region: Marks all columns in the selected region with vertical box.
Tolower Selected Region: Converts all sequences in the selected region to lower case.
Toupper Selected Region: Converts all sequences in the selected region to upper case.
Comment Selected Region: Add comment to the selected region. Comment will not be shown in the view, but will pop up in a tooltips when the region is pointed by the pointer.
Delete Comment of Selected Region: Add comment of the selected region.
Delete All Gap Items: Deletes sequences that are all gaps.
Delete All Gap Columns: Deletes columns that are all gaps.
Search Sequence: Search sequence inside a specified item.
Delete Base: Delete the base following the cursor if in "Single Sequence" Mode and "Insert" mode is "On". Replace the base following the cursor with "-" if in "Single Sequence" Mode and "Insert" mode is "Off". Deletes the column following the cursor if in "Whole Alignment" Mode and "Insert" Mode is "On". Replaces the column following the cursor with "-" if in "Whole Alignment" Mode and "Insert" Mode is "Off". Shortcut key "Del". Shortcut key "Del".
Position Comparison: Calculates the positions of a target sequence based on positions of the index item.
Search Item by Name: Search the item name by keyword. The first hit will be highlighted.
Sequence Extraction: Extracts a sub sequence from the selected item.
Deselect Selected Item: Marks the selected item as unselected, cancels the highlight.
Delete Selected Item: Deletes the selected item from the alignment.
Exported Selected Item: Exports the selected item to a specified directory.
Rename Selected Item: Renames the selected item.
Duplicate Selected Item: Adds a copy of the selected item to the alignment. For example, if the selected item named "strain1", then the duplicated sequence will be named "strain1_copy".
Move Selected Item to Top: Moves the selected item to the top of the alignment when showing in the view.
Move Selected Item to Bottom: Moves the selected item to the bottom of the alignment when showing in the view.
Move Selected Item Upward: Moves the selected item one position upward of the alignment when showing in the view.
Move Selected Item Downward: Moves the selected item one position downward of the alignment when showing in the view.
Sequence Variation Comparison: Compares the sequence variation pattern of a specified region of the alignment.
Pick Redundant Items: Calculates and reports all redundant sequences in the alignment.
Calculate Sequence Differences: Calculates and reports the sequence differences as a matrix between every two sequences in the alignment.
Translate All to Protein (DNA/RNA Alignment View): Translates all sequences into protein sequences.
Enzyme Sites of All Sequences: List all enzyme cutting sites of the alignment.These enzyme cutting sites are universal to all aligned sequences. In the followed dialog:
- Index Item: Specify a item for reporting the enzyme position, however the postion of the alignment of the enzyme site will also be reported.
- All: Reports all enzymes that have cutting sites on the alignment.
- Cut Once: Reports only enzymes that have one cutting site on the alignment.
- No Cut: Reports only enzymes that have NO cutting site on the alignment.
- Cut Multi Times: Reports only enzymes that have more than one cutting site on the alignment.
- Dot Plot: If checked, the view mode is "Dot Plot". All nucleotide and amino acid which are the same with the top sequence will be showed as a dot. This is convenient for observing the variations.
- Full Sequence: If checked, the view mode is "Full Sequence". Comapred to the "Dot Plot" mode, all nucleotide and amino acid will be showed without comparison with the top sequence.
- Hide: The tooltips will not shown.
- Show: A tooltips will follow the pointer showing the comments. If no comments at the pointed position, current position of pointed sequence and the alignment will be shown.
Demark Selected Region: Clear all annotations including comments, lines of the selected region.
Demark All Annotations: Clear all annotations including comments, lines of the whole alignment.
Page Up: If available, move the view one page up.
Page Down: If available, move the view one page down.
Page Left: If available, move the view one page to the left.
Page Right: If available, move the view one page to the right.
Scroll to the Top: If available, scrolls the view to the toppest position.
Scroll to the Bottom: If available, scrolls the view to the bottom position.
Scroll to the Beginning: If available, scrolls the view to the leftest position.
Scroll to the End: If available, scrolls the view to the rightest position.
Save Current View Options: Saves current settings as default, including the current size of the view, left and right frame width and the default recent file number showed in the recent file list.
View Options: Customizes the default size of the view, left and right frame width and the default recent file number showed in the recent file list.
BSEdit Shortcut List Table
|Ctrl + S||Save|
|Ctrl + N||Create a New Alignment|
|Ctrl + O||Open Alignemnt|
|Shift + Right Arrow||Select Next Base|
|Shift + Left Arrow||Deselect Previous Base|
|Shift + Down Arrow||Select Lower Item Base|
|Shift + Up Arrow||Deselect Upper Item Base|
|Ctrl + X||Deselect Selected Areas|
|Ctrl + C||Copy Selected Region|
|Ctrl + P||Print into PNG Picture File|
|Ctrl + Left Arrow||Scroll Leftward|
|Ctrl + Right Arrow||Scroll Rightward|
|Ctrl + Up Arrow||Scroll Upward|
|Ctrl + Down Arrow||Scroll Downward|
|Alt + Left Arrow||Scroll One Page Leftward|
|Alt + Right Arrow||Scroll One Page Rightward|
|Alt + Up Arrow||Scroll One Page Upward|
|Alt + Down Arrow||Scroll One Page Downward|
|Delete||Delete Next Base|
|Page Up||Scroll One Page Upward|
|Page Down||Scroll One Page Downward|
|Home||Scroll to the Left Most|
|End||Scroll to the Right Most|
|Alt + F4||Close Alignment|
|F2||Rename Selected Item|
|Ctrl + M||Shift between Single Sequence and Whole Alignment Edit Mode|
|F1||Show This Shortcut List Table|