Evolutionary Tree: Difference between revisions
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[[ | '''BACKGROUND''' | ||
[[Image:Cladogram view.JPG]] | |||
-> This is the cladogram treeview of SNAP-gamma protein. However, this view is not suitable enough to represent the evolutionary gap between species. | |||
In detecting evolunationary tree, BLAST was used to searching homologous sequence and to obtain the Batch Entrez IDs of the homologous gene. In addition, Clustal X was used to align the sequence specifically by using multiple alignment method. Phylogenetic analysis was conducted using treeview program follows with editing the tree to adding the boostrap value. | |||
---- | ---- | ||
'''FINAL TREE ANALYSIS''' | |||
[[Image:Rad.JPG]] | |||
-> Evolutionary analysis of the tree with radial view (for professional viewer) ] | |||
Legends: | Legends: | ||
* | * Red-dotted sign means boostrap value more than 75.00 or 75% | ||
* any number (in red) located near branching tree indicated boostrap value of the branching tree | |||
* Green Line: The species belongs to Plants group | |||
* Brown Line: Amoeba group | |||
* Purple Line: Parasite type | |||
* Pink Line : The species belongs to Insects Group | |||
* Light Green Line: Worms Group | |||
* Dark Blue Line: Invertebrate | |||
* Red Line: Vertebrate | |||
Other version: [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Rad2.JPG Evolutionary analysis of the tree with radial view (for non-professional or common viewer) ] | |||
---- | |||
'''IN DEPTH UNDERSTANDING''' | |||
SNAP-gamma protein evolutionary tree mostly contains more than 75% boostrapvalue. Thus, red dot signs was assign to represent more than 75% boostrap value. The value was indicated the degree of confidence about the branching order. As an example: in the diagram above, there is 39.0 boostrap value in branching ''Apis melifera'' and ''Tribolium castaneum''. The boostrap value is below 75%, thus it could be concluded that the degree of confidence of branching tree in the correct order is far below 95%. On the other hand, boostrap value more than 75% or 75.00 means 95% confidence that the branching tree is in the correct order | |||
As indicated in diagram above, SNAP-gamma protein was evolved in eukaryotes. There is no prokaryotes detected in the phylogenetic tree. | |||
Function (in various organism) = T.B.A - wait for Justine to assign the function (Overlap topic) | |||
Thus, it could be concluded that SNAP-gamma protein is important protein in eukaryotes animal. | |||
---- | |||
'''OTHER ATTRIBUTES''' | |||
[[command BLAST]] | |||
[[List IDs use as an batch entrez input]] | |||
[[List of various alignments of protein]] | |||
[[Boostrap value]] | |||
Latest revision as of 06:31, 5 June 2007
BACKGROUND
-> This is the cladogram treeview of SNAP-gamma protein. However, this view is not suitable enough to represent the evolutionary gap between species.
In detecting evolunationary tree, BLAST was used to searching homologous sequence and to obtain the Batch Entrez IDs of the homologous gene. In addition, Clustal X was used to align the sequence specifically by using multiple alignment method. Phylogenetic analysis was conducted using treeview program follows with editing the tree to adding the boostrap value.
FINAL TREE ANALYSIS
-> Evolutionary analysis of the tree with radial view (for professional viewer) ]
Legends:
- Red-dotted sign means boostrap value more than 75.00 or 75%
- any number (in red) located near branching tree indicated boostrap value of the branching tree
- Green Line: The species belongs to Plants group
- Brown Line: Amoeba group
- Purple Line: Parasite type
- Pink Line : The species belongs to Insects Group
- Light Green Line: Worms Group
- Dark Blue Line: Invertebrate
- Red Line: Vertebrate
Other version: Evolutionary analysis of the tree with radial view (for non-professional or common viewer)
IN DEPTH UNDERSTANDING
SNAP-gamma protein evolutionary tree mostly contains more than 75% boostrapvalue. Thus, red dot signs was assign to represent more than 75% boostrap value. The value was indicated the degree of confidence about the branching order. As an example: in the diagram above, there is 39.0 boostrap value in branching Apis melifera and Tribolium castaneum. The boostrap value is below 75%, thus it could be concluded that the degree of confidence of branching tree in the correct order is far below 95%. On the other hand, boostrap value more than 75% or 75.00 means 95% confidence that the branching tree is in the correct order
As indicated in diagram above, SNAP-gamma protein was evolved in eukaryotes. There is no prokaryotes detected in the phylogenetic tree.
Function (in various organism) = T.B.A - wait for Justine to assign the function (Overlap topic)
Thus, it could be concluded that SNAP-gamma protein is important protein in eukaryotes animal.
OTHER ATTRIBUTES
List IDs use as an batch entrez input
