Menu items

File menu


Load data from the specified server or the local file system. See the "Starting AlignmentViewer " section.


Print out the image of the current alignment display.


Configure user property parameters. See the "Configuring AlignmentViewer " section.


Exit the program. This item appears only in the standalone application. For applet version, you must exit the web browser to exit the program.

Search menu

Mark genes

Mark a specified set of genes.

An input form is opened for users to enter a list of gene names to be marked. Gene names can be entered individually or be read from a file. By pressing the Search button, gene names are registered. Locations of the registered genes are indicated on each axis of the dotplot display, and a new table window is opened containing the information of the these genes.

Additional calls of this function will add genes to the existing list. To remove genes from the list, enter the gene names to be removed and press Clear. To clear the entire list, press All Clear.

Figure 10. Marking genes. Input form for entering genes (A) and the dotplot with genes marked with triangles on each axis (B)

Filter Alignments

Filtering out the alignments that do not satisfy the specified conditions. Alignments are filtered from both the alignment and dotplot displays. A filter can be applied to one of the following fields:

  • Identity: percentage identity; numeric.

  • Score: similarity score; numeric.

  • Best Hit Status: one of the following: 3, orthologs (bidirectional best hits, BBH); 2, duplicated only in the sequence-2; 1, duplicated only in the sequence-1; 0, paralogs.

For specification of the numeric field conditions, see the next subsection "Filter Genes/Segments "

Once filtered, a '*' mark is displayed on the left side of the alignment track (see Figure 11C). Additional calls will add filters to the existing one. For example, users can specify conditions such as "Best Hit Status is BBH and Identity ≥ 90%" by two successive calls of this function. To reset the filters, press the Reset Alignment Filters button.

Figure 11. Filtering alignments. The filtering condition window (A), and alignment displays of before (B) and after (C) filtering (showing only BBH).

Filter Genes/Segments

Filtering out the genes or feature segments that do not satisfy the specified conditions. A filter can be applied to any field of any kind of segment that is currently loaded.

Kinds of conditions to be applied are different depending on the types of the fields (numeric and string). The following conditions are defined:

Numeric field

Available conditions are: Between (a ≤ x ≤ b), Except Between(x < a or b < x), Less Than (x < a), Less Equal (x ≤ a), Equal (x = a), Greater Equal (x ≥ a), and Greater Than (x > a), where a and/or b are values to be specified. To specify Between or Except Between, two values should be separated by a comma (e.g. "80,90").

String field

Available conditions are Regex (regular expression) and Equal (exact match).

Once filtered, a '*' mark is displayed on the left side of the annotation track. Additional calls will add filters to the existing one. To reset the filter on the specified segment, choose the segment type and press the Reset This Filter button. To reset all filters, press the Reset All Filters button.

Figure 12. Filter genes/alignments

Dynamic Search

Search each genome for specific segments or sets of segments dynamically, by calling a CGI script running on the server. Results will be displayed in the additional annotation tracks, or in the outermost pair of tracks (overwriting the existing data) if the maximum number of segment tracks have already been used.

Currently, the following programs are available:

  • Blast: BLAST similarity search for a nucleotide [blastn(direct) / tblastx(translation)] or a protein [tblastn] query sequence.

  • PatSearch: Regular expression pattern search. See the document of the Java regex library.

  • DirRep: Direct repeat search.

  • SimpleRep: Simple repeat (or short tandem repeat) search.

View menu

Gene/Segment Data Table

Show table of genes or specified feature segment on the specified genome. In the table, each row contains species name, the beginning position, the ending position, strand direction, assigned color, and the name of the segment. Additional fields are added, if any, depending on the segment type. By clicking a row of this table, the current scope is reset such that the specified gene or segment is centered.

Figure 13. Gene table

Sequence Window

Show nucleotide sequence of each genome within the current region.

Exchange Reference Genome

Exchange the reference and the target sequences. Both the alignment and dotplot displays are changed.