Materials and Methods: Difference between revisions
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==''' | =='''Sequence Homology'''== | ||
Blast programme was used to carry out amino acid sequence similarity searches, with the query sequence. This was done using a fixed database stored within a DVD-Rom. | |||
Return to '''[[Evolution]]''' | |||
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=='''Multiple Sequence Alignments (msa)'''== | =='''Multiple Sequence Alignments (msa)'''== | ||
Sequence alignment was performed using ClustalX. Similarly, the ClutalX programme used for this was obtained from the DVD-Rom. | |||
Return to '''[[Evolution]]''' | |||
=='''Phylogenetic Map (Tree)'''== | |||
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Treeview programme was used to view the final tree. | Treeview programme was used to view the final tree. | ||
Return to '''[[Evolution]]''' | |||
=='''Bootstrapping'''== | |||
Seqboot (within Phylip) was used to replicate 100 samples of the sequence alignments. | |||
The outfile (.aln) was then used in calculating the bootstrap distance matrices, using Prodist. The parameter setting for this calculation was similar to the initial distance matrix calculation, using PAM-Dayhoff method. An added parameter was including multiple data sets, of 100 replicates. | |||
This outfile (.dis) was run through Neighbor. The parameter settings were again similar to the previous generation of the earlier phylogenetic tree. An added parameter, as was with the bootstrap distance matrix calculations, was the inclusion of multiple data sets of 100 replicates. | |||
The treefile (.ph) was run through Consense (within Phylip) to obtain the final bootstrapped phylogenetic tree. Bootstrap branch values were also obtained to determine the reliability of the tree branches. | |||
Return to '''[[Evolution]]''' | Return to '''[[Evolution]]''' | ||
Latest revision as of 18:27, 10 June 2007
Sequence Homology
Blast programme was used to carry out amino acid sequence similarity searches, with the query sequence. This was done using a fixed database stored within a DVD-Rom.
Return to Evolution
Multiple Sequence Alignments (msa)
Sequence alignment was performed using ClustalX. Similarly, the ClutalX programme used for this was obtained from the DVD-Rom.
Return to Evolution
Phylogenetic Map (Tree)
Phylip programme was used for the purpose of obtaining a phylogentic tree to determine the relationship of the proteins from individual organisms.
The various programmes used were again obtained from the DVD.
Prodist (within Phylip) was used to calculate the distance matrix. The calculation method selected was as using PAM-Dayhoff.
Neighbor (also found within Phylip) was next used to form the phylogenetic tree, using the distance matrix calculation obtained. The “Input order of species” option was set to “Random” when generating the tree, with a random odd number also given.
Treeview programme was used to view the final tree.
Return to Evolution
Bootstrapping
Seqboot (within Phylip) was used to replicate 100 samples of the sequence alignments.
The outfile (.aln) was then used in calculating the bootstrap distance matrices, using Prodist. The parameter setting for this calculation was similar to the initial distance matrix calculation, using PAM-Dayhoff method. An added parameter was including multiple data sets, of 100 replicates.
This outfile (.dis) was run through Neighbor. The parameter settings were again similar to the previous generation of the earlier phylogenetic tree. An added parameter, as was with the bootstrap distance matrix calculations, was the inclusion of multiple data sets of 100 replicates.
The treefile (.ph) was run through Consense (within Phylip) to obtain the final bootstrapped phylogenetic tree. Bootstrap branch values were also obtained to determine the reliability of the tree branches.
Return to Evolution
