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Java Viewer of Alignment Results DBSCAN and SCAN2 Programs

(Scan-2 and DBscan programs are genomic sequence comparison programs based on new fast algorithm developed in Softberry Inc.)

The viewer has four main panels:

General View Panel (Top of the viewer window)
Selected Alignment Panel (Middle of the window)
Alignnment Selection Panel (Bottom of the window)
Output Message Panel (one-line panel at the very bottom of the window).

General View Panel

Graphical view of full-length alignment is drawn as two horizontal bars, each representing one sequence. High homology regions are drawn in red, regions of low or no homology - in yellow, and stretches of one sequence opposite to gaps in another sequence are drawn in gray. Pink homology profile is located above an alignment.

There are two horizontal scroll bars at the bottom of the panel: first one is a regular scroll bar, the second one is for zooming an alignment in and out.

When mouse cursor points to one of the bars, information about the region is displayed in Output Message panel: homology percentage, length, coordinates of start of the region on first and and second sequence. You can select a region on alignment by pressing left mouse button and dragging. Aligned sequence of selected region will be displayed in Detail View panel. Marking a region by Shift+Click opens selected sequence in a separate browser window, from where it can be saved or copied to other applications.

Detail View Panel

Panel contains nucleotide or amino acid alignment of selected region. Length of output line can be changed through Main MenuOption, Set Output Alignment Length.

Alignnment Selection Panel

For DBSCAN program, this panel has five fields: Selection List window, Forward button, Back button, and Alignment Info button.

Selection List field displays list of sequences homologous to the query sequence. The top sequence has most homology, the bottom sequence has least. Forward/Back buttons display next/previous 700 entries in Selection List window. Doubleclicking on a particular entry in Selection List displays alignment of that entry with query sequence in General View panel. Alignment Info button opens a window with general information on selected alignment (score, lengths of sequences, number of blocks etc.)

For SCAN2 program, Alignnment Selection Panel consists only of Alignment Info button.

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