Tomato-Utricularia Syntenic Depth: Difference between revisions
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Using v4 of the Utricularia genome (http://genomevolution.org/CoGe//OrganismView.pl?dsgid=19456) | Using v4 of the Utricularia genome (http://genomevolution.org/CoGe//OrganismView.pl?dsgid=19456) | ||
==4 genes in 80== | ==4 genes in an 80 gene window== | ||
SynFind: http://genomevolution.org/r/4tqx | SynFind: http://genomevolution.org/r/4tqx | ||
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Depth 10 2 of 19459 0.01% | Depth 10 2 of 19459 0.01% | ||
==4 genes in 40== | ==4 genes in a 40 gene window== | ||
SynFind: http://genomevolution.org/r/4tqi | SynFind: http://genomevolution.org/r/4tqi | ||
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Depth 5 25 of 8468 0.30% | Depth 5 25 of 8468 0.30% | ||
Depth 6 5 of 8468 0.06% | Depth 6 5 of 8468 0.06% | ||
==Materials and Methods== | |||
Syntenic Depth tables are calculated by CoGe's tool [[SynFind]]. These analyses used Last <ref name="last">{{cite journal |author=Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., and Frith, M. C. |title=Adaptive Seeds Tame Genomic Sequence Comparison |journal=Genome Res | volume=21 |pages=487-493 |year=2011 }}</ref> to compare protein coding sequences (default parameters) of these genomes and Synteny_Score (of the TangTools <ref name=synteny_score>{{cite journal |author=Haibao Tang |title=TangTools | url=https://github.com/tanghaibao/quota-alignment }}</ref> software package) to identify syntenic regions (gene window size =80, minimum number of genes =4; collinear scoring function). | |||
===References=== | |||
{{reflist}} | |||
Latest revision as of 22:14, 20 June 2012
Follow this link for information on Syntenic depth.
Syntenic depth measurements permit classifying the number of whole genome duplications that have happened in one lineage relative to another. Unfortunately, these analyses are not 100% conclusive, but provide supporting evidence, especially when combined with Syntenic dotplots.
Using v4 of the Utricularia genome (http://genomevolution.org/CoGe//OrganismView.pl?dsgid=19456)
4 genes in an 80 gene window
SynFind: http://genomevolution.org/r/4tqx
Utricularia gibba
Depth 1 6972 of 19459 35.83% Depth 2 4727 of 19459 24.29% Depth 3 3392 of 19459 17.43% Depth 4 2153 of 19459 11.06% Depth 5 1230 of 19459 6.32% Depth 6 603 of 19459 3.10% Depth 7 223 of 19459 1.15% Depth 8 118 of 19459 0.61% Depth 9 39 of 19459 0.20% Depth 10 2 of 19459 0.01%
4 genes in a 40 gene window
SynFind: http://genomevolution.org/r/4tqi
Utricularia gibba
Depth 1 5566 of 8468 65.73% Depth 2 2071 of 8468 24.46% Depth 3 664 of 8468 7.84% Depth 4 137 of 8468 1.62% Depth 5 25 of 8468 0.30% Depth 6 5 of 8468 0.06%
Materials and Methods
Syntenic Depth tables are calculated by CoGe's tool SynFind. These analyses used Last [1] to compare protein coding sequences (default parameters) of these genomes and Synteny_Score (of the TangTools [2] software package) to identify syntenic regions (gene window size =80, minimum number of genes =4; collinear scoring function).
References
- ↑ Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., and Frith, M. C. (2011). "Adaptive Seeds Tame Genomic Sequence Comparison". Genome Res 21: 487-493.
- ↑ Haibao Tang. TangTools. https://github.com/tanghaibao/quota-alignment.