The Alignment Explorer provides options to (1) view and manually edit alignments and (2) generate alignments using a built-in CLUSTALW implementation (for the complete sequence or data in any rectangular region). The Alignment Explorer also provides tools for exploring web-based databases (e.g., NCBI Query and BLAST searches) and retrieving desired sequence data directly into the current alignment.
The Alignment Explorer has the following menus in its main menu: Data, Edit, Search, Alignment, Web, Sequencer, Display, and Help. In addition, there are Toolbars that provide quick access to many Alignment Explorer functions. The main Alignment Explorer window contains up to two alignment grids.
For amino acid input sequence data, the Alignment Explorer provides only one view. However, it offers two views of DNA sequence data: the DNA Sequences grid and the Translated Protein Sequences grid. These two views are present in alignment grids in the two tabs with each grid displaying the sequence data for the current alignment. Each row represents a single sequence and each column represents a site. A "*" character is used to indicate site columns, exhibiting consensus across all sequences. An entire sequence may be selected by clicking on the gray sequence label cell found to the left of the sequence data. An entire site may be selected by clicking on the gray cell found above the site column. The alignment grid has the ability to assign a unique color to each unique nucleotide or amino acid and it can display a background color for each cell in the grid. This behavior can be controlled from the Display menu item found in the main menu. Please note that when the ClustalW alignment algorithm is initiated, it only will align the sites currently selected in the alignment grids. Multiple sites may be selected by clicking and then dragging the mouse within the grid. Note that all of the manual or automatic alignment procedures carried out in the Protein Sequences grid will be imposed on the corresponding DNA sequences as soon as you flip to the DNA sequence grid. Even more importantly, the Alignment Explorer provides unlimited UNDO capabilities.