Difference between revisions of "Syntenic dotplot"
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'''Syntenic dotplots''' are a type of scatter-plot. Each axis represents a sequence laid end-to-end, and each dot in the scatter-plot represents a putative [[Homologous]] match between the two sequences. Often, these dotplots are used for whole genome comparisons within the same genome or across two genomes from different taxa in order to identify [[Synteny]]. Synteny is defined as two or more genomic regions that are derived from a common ancestral genomic region. The evidence for synteny is the identification of a set of genes in each genome that have a collinear arrangement. When such a pattern of gene-order conservation is discovered, the most parsimonious explanation is that the two regions are related through a common ancestor. While syntenic dotplots are useful for identifying related genomic regions, they are also useful for identifying genomic regions that have undergone an evolutionary change in one of the two genomes being compared. For example, insertions, deletions, duplications, and inversions are readily identifiable from these plots. | '''Syntenic dotplots''' are a type of scatter-plot. Each axis represents a sequence laid end-to-end, and each dot in the scatter-plot represents a putative [[Homologous]] match between the two sequences. Often, these dotplots are used for whole genome comparisons within the same genome or across two genomes from different taxa in order to identify [[Synteny]]. Synteny is defined as two or more genomic regions that are derived from a common ancestral genomic region. The evidence for synteny is the identification of a set of genes in each genome that have a collinear arrangement. When such a pattern of gene-order conservation is discovered, the most parsimonious explanation is that the two regions are related through a common ancestor. While syntenic dotplots are useful for identifying related genomic regions, they are also useful for identifying genomic regions that have undergone an evolutionary change in one of the two genomes being compared. For example, insertions, deletions, duplications, and inversions are readily identifiable from these plots. | ||
| − | Below is an example of comparing two closely related substrains of E. coli strain K12. While their entire genome is highly similar to one another at the nucleotide identity level, there are many "breaks" in the syntenic path through their genomes which reveal a variety of genomic changes (mostly insertions and deletions for this example). | + | Below is an example of comparing two closely related substrains of E. coli strain K12. While their entire genome is highly similar to one another at the nucleotide identity level, there are many "breaks" in the syntenic path through their genomes which reveal a variety of genomic changes (mostly insertions and deletions for this example). |
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| + | [[Image:Dotplot.png|thumb|right|600px| Syntenic dotplot of E-coli B strain REL606(x-axis) and E-coli K12 strain DH10B (y-axis). The "green" line represents the regions of similarities between the two genomes while the discontinuities in the dotplot represent regions of genetic variations at a given locus between the two substrains of E-coli. The numbers correspond to the individual analysis of a break provided in the table below. This dotplot can be regenerated [http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=7454;dsgid2=4241;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder here] by entering the name of these substrains from the organism database.]] | ||
Revision as of 12:43, 12 February 2010
Syntenic dotplots are a type of scatter-plot. Each axis represents a sequence laid end-to-end, and each dot in the scatter-plot represents a putative Homologous match between the two sequences. Often, these dotplots are used for whole genome comparisons within the same genome or across two genomes from different taxa in order to identify Synteny. Synteny is defined as two or more genomic regions that are derived from a common ancestral genomic region. The evidence for synteny is the identification of a set of genes in each genome that have a collinear arrangement. When such a pattern of gene-order conservation is discovered, the most parsimonious explanation is that the two regions are related through a common ancestor. While syntenic dotplots are useful for identifying related genomic regions, they are also useful for identifying genomic regions that have undergone an evolutionary change in one of the two genomes being compared. For example, insertions, deletions, duplications, and inversions are readily identifiable from these plots.
Below is an example of comparing two closely related substrains of E. coli strain K12. While their entire genome is highly similar to one another at the nucleotide identity level, there are many "breaks" in the syntenic path through their genomes which reveal a variety of genomic changes (mostly insertions and deletions for this example).
