Syntenic path assembly: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
|||
| Line 3: | Line 3: | ||
This algorithm also works quite well in aligning a WGS assembly between distally related organisms. See below for examples. | This algorithm also works quite well in aligning a WGS assembly between distally related organisms. See below for examples. | ||
===Definitions=== | |||
*WGS: [[Whole-genome shotgun]] | |||
[[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]]]] | ||
| Line 14: | Line 17: | ||
== | ==Tetraodon (puffer fish): Takifugu rubripes and Tetraodon nigroviridis== | ||
<gallery widths =500px heights=500px compation="Syntenic Path Assembly in SynMap of distally related puffer fish"> | <gallery widths =500px heights=500px compation="Syntenic Path Assembly in SynMap of distally related puffer fish"> | ||
File:Screen shot 2011-02-18 at 1.52.19 PM.png|Syntenic dotplot using [[SynMap]] between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). (Fugu is a WGS assembly.) '''Note:''' the background is colored black due to the number of contigs in the WGS assembly. Each contig/chromosome is visually separated from one another by a vertical or horizontal black line. Results may be regenerated at http://genomevolution.org/r/2k7b | File:Screen shot 2011-02-18 at 1.52.19 PM.png|Syntenic dotplot using [[SynMap]] between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). (Fugu is a WGS assembly.) '''Note:''' the background is colored black due to the number of contigs in the WGS assembly. Each contig/chromosome is visually separated from one another by a vertical or horizontal black line. Results may be regenerated at http://genomevolution.org/r/2k7b | ||
| Line 23: | Line 26: | ||
==Carnivora: Giant Panda (WGS Assembly) to Dog (reference genome)== | ==Carnivora: Giant Panda (WGS Assembly) to Dog (reference genome)== | ||
<gallery widths =500px heights=500px compation="Syntenic Path Assembly in SynMap of distally related mammals"> | <gallery widths =500px heights=500px compation="Syntenic Path Assembly in SynMap of distally related mammals"> | ||
File:Screen shot 2011-02-19 at 6.17.08 PM.png|Syntenic dotplot by SynMap of WGS giant panda genome (x-axis) versus complete dog genome(y-axis): http://genomevolution.org/r/2kbv | |||
File:Screen shot 2011-02-19 at 6.09.11 PM.png|[[SynMap]] Syntneic path assembly of WGS giant panda genome (x-axis) to complete dog genome (y-axis). Results may be regenerated at: http://genomevolution.org/r/2kbt . '''Note:''' the background is colored black due to the number of contigs in the WGS assembly. Each contig/chromosome is visually separated from one another by a vertical or horizontal black line. | File:Screen shot 2011-02-19 at 6.09.11 PM.png|[[SynMap]] Syntneic path assembly of WGS giant panda genome (x-axis) to complete dog genome (y-axis). Results may be regenerated at: http://genomevolution.org/r/2kbt . '''Note:''' the background is colored black due to the number of contigs in the WGS assembly. Each contig/chromosome is visually separated from one another by a vertical or horizontal black line. | ||
</gallery> | </gallery> | ||
Revision as of 00:52, 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.
Definitions
- WGS: Whole-genome shotgun
E. coli
- Syntenic Path Assembly in SynMap of E. coli
-
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
Tetraodon (puffer fish): Takifugu rubripes and Tetraodon nigroviridis
-
Syntenic dotplot using SynMap between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). (Fugu is a WGS assembly.) Note: the background is colored black due to the number of contigs in the WGS assembly. Each contig/chromosome is visually separated from one another by a vertical or horizontal black line. 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
Carnivora: Giant Panda (WGS Assembly) to Dog (reference genome)
-
Syntenic dotplot by SynMap of WGS giant panda genome (x-axis) versus complete dog genome(y-axis): http://genomevolution.org/r/2kbv -
SynMap Syntneic path assembly of WGS giant panda genome (x-axis) to complete dog genome (y-axis). Results may be regenerated at: http://genomevolution.org/r/2kbt . Note: the background is colored black due to the number of contigs in the WGS assembly. Each contig/chromosome is visually separated from one another by a vertical or horizontal black line.
