To resolve the problem of visualization of synteny within a large set of genomic fragments, we suggest a method based on reconstruction and visualization of graphs representing the relationships between genomic fragments. The method is based on building a directed, weighted, bipartite graph, nodes of which represent contigs, and the weights of edges denote the coverage of contigs' pairwise alignments.
The image below shows a graph representing relationships between genomic fragments.
The nodes representing targeted contigs are shown in gray, while those representing query contigs are colored.
The color of query contigs' nodes varies in the spectrum from red to blue, depending on alignment coverage.
A table in a top left corner contains some information about contigs:
To move several contigs, first select them with a mouse and then drag.
To restore initial scale, use a button
A selected contig will be marked yellow.
Selected contigs will be marked yellow.
Via Circosa pie charts allow detailed visualization of relationships between several contigs.
Target contigs are shown in gray, query contigs are colored.
The color of links (blocks of alignment) varies in the spectrum from red to blue, depending on the coverage.
A table in a top left corner contains a list of contigs and their coverage.