Following is a quick tour of the many displays and queries available through SyMAP.

Whole genome views Circle Dot Plot Block

Chromosome Explorer Circle Dot Plot 2D Base View

Query Interface Query Result Multiple Alignment Click any image for a close-up view

Whole genome views

Circle

DotPlot

Block

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SyMAP can be used to query and view multiple synteny genome pairs at once (2-3 is best). The synteny can be viewed from the Project Manager. All projects in the database will be listed on the left panel.

Selecting projects on the left panel shows them on the right panel. A check mark in the Available Syntenies matrix indicates pairs that have computed synteny that can be viewed. These can be viewed from the lower multi-genome Display for All Pairs options.

By selecting a cell with synteny, the Display for Selected Pair buttons are activated, which display synteny views for the two-genome.

The Project Manager

The Circle view shows two genomes.

The Dot plot can show two or more genomes where the image on the lower left shows three.
A cell can be clicked to view a chromosome x chromosome Dot plot, from which a 2D view can be displayed.

The Block view shows two genomes.
Clicking a chromosome shows a close-up of it, where a block can be clicked to view the 2D display of it.

Chromosome Explorer

Circle & DotPlot

2D 3-Chr

Base View

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The Chromosome Explorer provides multi-chromosome views for multi-genomes.

Multiple chromosomes can be selected from different species on the left-hand panel.

The default display is the Circle view shown. From here, one can select Dot Plot or 2D.

2D 3-Chr

This is a three-chromosome view. The dark blue and purple down the center of the chromosomes are annotated exons, where blue is positive strand and purple is negative strand. The brown and green lines between chromosomes are hit-wires connecting similar regions on the two chromosomes. The brown are hit-wires with the same orientation on both connecting chromosomes and the green are different orientation. Only hits that are part of a synteny block are shown here.

2D Closeup

The image on the right shows a smaller region with the Annotation option is turned on. A gene can be right clicked to view a popup of extended information, including the exons and hits. The hit-wire can be right clicked to view of popup of details of its information.

Base View

It is possible to zoom in even further and see a basepair-alignment of the hits in the region.

Query Interface

Results

MSA

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SyMAP includes powerful search features to help make the most of synteny information.

Query Results

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The query results table has full flexibility in column selection and ordering.

Multiple alignment

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By selecting a one or more rows, the genes sequences can be aligned using MUSCLE or MAFFT (Refs^6,7).

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Email Comments To: symap@agcol.arizona.edu