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IMC has various display windows as follows.
It is a viewer / editor prepared for genome annotation.
It is a window independent from the main window.
Multiple Linear Genome Map Viewer is a viewer that compares annotation such as genes of multiple closely related species genomes in parallel for each genome in parallel and is docked in the IMC main window.
We call aliases as linear genome map viewer, reference genome map, reference map etc.
Circular Genome Map (Circular Genome Map) is a function to compare and draw Features and Contents from arbitrary genomic chromosomes or genomic chromosomes of closely related species and arbitrary numerical data specific to genome position on concentric circles.
You can display distribution status of each gene such as genes of each genomic chromosome, change of base composition, etc.
The order of concentric circles of features and content profiles to be placed can be changed arbitrarily.
Drawing parameter setting can be changed for each concentric circle.
It is also possible to change the diameter of the circular genome map and the printing parameters.
For printing a circular genome map, in addition to direct printing, you can output files in PDF, PNG, and EMF formats.
A large number of features drawn on the concentric circle of the circular genome map can be classified and displayed in different colors depending on the annotation type if there are annotations.
Sequence files drawn on the circular genome map are referenced in the order shown in the main current directory. For this reason it is easy to manipulate drawing a number of different circular genome sequences in the same format.
By clicking on a part of the circular genome map it is possible to display the area of the corresponding main feature map.
In the circular genome map, the sequence file name and total base length (when single genomic chromosome) are drawn at the center, and the base number scale is displayed around it.
The starting position base of the scale can also be changed.
The map layout can be registered as a layout style, and the registered circular genome layout style can be called later.
It is a viewer / editor which is used when reading output file from ABI, SCF capillary sequencer.
Displays not only the base sequence but also the trace waveform.
The description window is a window for entering and editing values in the feature's Qualifier.
Launched with a right click on the feature and you can edit all the Qualifiers for that feature.
Change the Position of the feature.
Change the Feature Key to which the feature belongs.
This is a viewer that displays profiles such as secondary structure of amino acid sequence in parallel. Total profile design and display, motif display and so on are possible.
Multiple alignment viewer is a window for displaying multiple alignment of DNA sequences and amino acid sequences.
Multiple alignment viewer can be launched from homology search result dialog etc.
Molecular phylogenetic tree viewer is a tool to draw molecular phylogenetic trees from sequences of such as genes.
This viewer can be launched from multiple alignment viewer.
Alignment Viewer is a viewer editor that displays the primary analysis result of GT and executes secondary analysis etc.
Alignment Viewer can be launched from GT's main window.
The Alignment Viewer consists of a menu bar, a tool box, and four panes.
Although the menu bar is fixed in the Viewer window, the toolbox and the four panes can be removed from the window and displayed at any position on the desktop.
The toolbox can also be hidden.
The four panes are named as Navigation Pane, Feature Pane, Consensus Pane and Fragment Pane from the top.
Navigation Pane is a special pane for navigating the other three panes and has a two-step scale of genome-wide scale and scale within the selected region.
Feature Pane has functions similar to IMC's main feature map and can perform most functions of IMC.
Consensus Pane is a function to display the Assembly result as a sequence alignment of Contig and Read constituting it, and a function to display the Mapping result as a sequence alignment of the reference genome sequence and Read.
Fragment Pane is a function to graphically display Consensus Pane, which allows you to view assemblies and mapping in a more bird's-eye view.
This is a window for drawing a restriction enzyme map.
It also draws a feature map similar to the main feature map.
Zoom, horizontal scroll, and gel electrophoresis diagrams are available.