Basic Functions
This prepares Alignment Builder for a new alignment. Any sequence data currently loaded into Alignment Builder is discarded.
This activates the Open File dialog window. It is used to send sequence data from a properly formatted file into Alignment Builder.
This activates the Save Alignment Session dialog window. It may be used to save the current state of the Alignment Builder into a file so that it may be restored in the future.
This causes nucleotide sequences currently loaded into Alignment Builder to be translated into their respective amino acid sequences.
Web Browser/Data Explorer Functions
This displays the NCBI BLAST web site in the integrated Web Browser window. If a sequence in the sequence grid is selected prior to clicking this button, the Web Explorer will auto-fill the BLAST query window with the selected sequence data.
This displays the default database (GenBank) in the integrated Web Browser window.
This activates the Open Trace File dialog window, which may be used to open and view a sequencer file. The sequence data from the sequencer file then can be sent into Alignment Explorer.
Alignment Functions
This displays the ClustalW parameters dialog window, which is used to configure ClustalW and initiate the alignment of the selected sequence data. If you do not select sequence data prior to clicking this button, a message box will appear asking if you would like to select all of the currently loaded sequences.
This displays the MUSCLE parameters dialog window, which is used to configure MUSCLE and initiate the alignment of the selected sequence data. If you do not select sequence data prior to clicking this button, a message box will appear asking if you would like to select all of the currently loaded sequences.
This marks or unmarks the currently selected single site in the alignment grid. Each sequence in the alignment may have only one site marked at a time. Modifications can be made to the alignment by marking two or more sites and then aligning them using the Align Marked Sites function.
This button aligns marked sites. Two or more sites must be marked in order for this function to have an effect.
Search Functions
This activates the Find Motif search box. When this box appears, it asks you to enter a motif sequence (a small subsequence of a larger sequence) as the search term. After the search term is entered, the Alignment Builder finds each occurrence of the search term and indicates it with yellow highlighting. For example, if you were to enter the motif “AGA” as the search term, then each occurrence of “AGA” across all sequences in the sequence grid would be highlighted in yellow.
This searches towards the beginning of the current sequence for the first occurrence of the motif search term. If no motif search has been performed prior to clicking this button, the Find Motif search box will appear.
This searches towards the end of the current sequence for the first occurrence of the motif search term. If no motif search has been performed prior to clicking this button, the Find Motif search box will appear.
This locates the marked site in the current sequence. If no site has been marked, a warning box will appear.
Editing Functions
This undoes the last Alignment Builder action.
This copies the current selection to the clipboard. It may be used to copy a single base, a block of bases, or entire sequences to the clipboard.
This removes the current selection from the Alignment Builder and sends it to the clipboard. This function can affect a single base, a block of bases, or entire sequences.
This pastes the contents of the clipboard into the Alignment Builder. If the clipboard contains a block of bases, it will be pasted into the builder starting at the point of the current selection. If the clipboard contains complete sequences they will be added to the current alignment. For example, if the contents of a FASTA file were copied to the clipboard from a web browser, it would be pasted into Alignment Builder as a new sequence in the alignment.
This deletes a block of selected bases from the alignment grid.
This deletes gap-only sites (sites containing a gap across all sequences in the alignment grid) from a selected block of bases.
Sequence Data Insertion Functions
This creates a new, empty sequence row in the alignment grid. A label and sequence data must be provided for this new row.
This activates an Open File dialog box that allows for the selection of a sequence data file. Once a suitable sequence data file is selected, its contents will be imported into Alignment Builder as new sequence rows in the alignment grid.
Site Number display on the status bar
Site #
The Site # field indicates the site represented by the current selection. If the w/o Gaps radio button is selected, then the Alignment Builder will disregard the shifting affect of gaps when determining gap sites. If a block of sites are selected, then this field will contain the site # for the first site in the block. If an entire sequence is selected this field will contain the site # for the last site in the sequence.