Phytanoyl-CoA method: Difference between revisions
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===Multiple Sequence Alignment=== | ===Multiple Sequence Alignment=== | ||
The original fasta sequence for the Phytanoyl-CoA hydroxylase protein was searched against the non-redundant databases of blast. From these results 49 other sequences were selected for comparison based on low e-values and to include diverse organisms. From these 4 were removed due in inappropriate length leaving a total of 46 sequences including the target sequence. These were then aligned using the default setting in ClustalX. The final alignment from the postscript output can be seen in Figure 1.1. | The original fasta sequence for the Phytanoyl-CoA hydroxylase protein was searched against the non-redundant databases of blast. From these results 49 other sequences were selected for comparison based on low e-values and to include diverse organisms. From these 4 were removed due in inappropriate length leaving a total of 46 sequences including the target sequence. These were then aligned using the default setting in ClustalX. The final alignment from the postscript output can be seen in [[Phytanoyl-CoA results#Multiple Sequence Alignment|Figure 1.1-3]]. | ||
===Phylogenetic Trees=== | ===Phylogenetic Trees=== | ||
Revision as of 11:32, 9 June 2008
Multiple Sequence Alignment
The original fasta sequence for the Phytanoyl-CoA hydroxylase protein was searched against the non-redundant databases of blast. From these results 49 other sequences were selected for comparison based on low e-values and to include diverse organisms. From these 4 were removed due in inappropriate length leaving a total of 46 sequences including the target sequence. These were then aligned using the default setting in ClustalX. The final alignment from the postscript output can be seen in Figure 1.1-3.
Phylogenetic Trees
The orginal tree was obtained by submitting the alignment file obtained from Clustal to the Phylodendron Web Form found at http://iubio.bio.indiana.edu/treeapp/ The data was also bootstrapped using the seqboot function in Phylip. Using the neighbor and consensus programs a consensus tree file was obtained and viewed using Phylodendron.
Abstract | Introduction | Results | Discussion | Conclusion | Method | References
