Syntenic path assembly: Difference between revisions
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==Overview== | ==Overview== | ||
The Syntenic Path Assembly is an option in [[SynMap]] to do a reference genome assembly of contigs using synteny to determine the order and orientation of the contigs. To use this option, select "Order contigs by best syntenic path" under the Display Options tab. | The Syntenic Path Assembly is an option in [[SynMap]] to do a reference genome assembly of contigs using synteny to determine the order and orientation of the contigs. To use this option, select "Order contigs by best syntenic path" under the Display Options tab. When an assembly is generated, you may download the assembled sequence (contigs are joined using 100Ns). | ||
This algorithm also works quite well in aligning a WGS assembly between distally related organisms. See below for examples. | |||
[[Image:Screen shot 2011-02-18 at 1.38.59 PM.png|thumb|500px|center|Selecting the Syntenic Path Assembly option in [[SynMap]]]] | [[Image:Screen shot 2011-02-18 at 1.38.59 PM.png|thumb|500px|center|Selecting the Syntenic Path Assembly option in [[SynMap]]]] | ||
[[Image:Screen shot 2011-02-18 at 1.58.23 PM.png|frame|center|running a syntenic path assembly in SynMap, there is an option to download the assembled sequence (contigs are joined using 100Ns).]] | [[Image:Screen shot 2011-02-18 at 1.58.23 PM.png|frame|center|running a syntenic path assembly in SynMap, there is an option to download the assembled sequence (contigs are joined using 100Ns).]] | ||
==E. coli== | ==E. coli== | ||
Revision as of 00:38, 20 February 2011
Overview
The Syntenic Path Assembly is an option in SynMap to do a reference genome assembly of contigs using synteny to determine the order and orientation of the contigs. To use this option, select "Order contigs by best syntenic path" under the Display Options tab. When an assembly is generated, you may download the assembled sequence (contigs are joined using 100Ns).
This algorithm also works quite well in aligning a WGS assembly between distally related organisms. See below for examples.
E. coli
- Syntenic Path Assembly in SynMap of E. coli
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SynMap analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis). Results may be regenerated at http://genomevolution.org/r/2k70 -
SynMap analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis) using SynMap's Syntenic Path Assembly to order contigs. Results may be regenerated at: http://genomevolution.org/r/2k71
Puffer fish: Takifugu rubripes and Tetraodon nigroviridis
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Syntenic dotplot using SynMap between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). Fugu is a WGS assembly. Results may be regenerated at http://genomevolution.org/r/2k7b -
Syntneic dotplot using SynMap between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis) using the Syntenic Path Assembly option. Fugu is a WGS assembly and fully syntenic converage to Tetraodon is detectable. Results may be regenerated at http://genomevolution.org/r/2k79
