DHRS1 Method: Difference between revisions
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==MULTIPLE SEQUENCE ALIGNMENT== | ==MULTIPLE SEQUENCE ALIGNMENT== | ||
The results from the blast search were then screened and a selection was of these results were used for a multiple sequence alignment using ClustalX. This result was boostrapped using 1000 simulations and these values checked and more sequences were added to improve the resolution of specific branches. A bootstrapped phylogram was produced | The results from the blast search were then screened and a selection was of these results were used for a multiple sequence alignment using ClustalX. This result was boostrapped using 1000 simulations and these values checked and more sequences were added to improve the resolution of specific branches. A bootstrapped phylogram was produced. | ||
==TREE VIEW== | |||
The results from ClustalX were imported into treeview and a phylogenetic tree was produced, with bootstrapping values attached, and then split into bacteria and anamalia kingdoms. | |||
==STRUCTURAL ALIGNMENT== | |||
The protien sequence from PDB (2qq5) was aligned aginst other known sequences for structural similarity using the Dali web server. The structure of the most structurally related protien (Oxoacyl-(Acyl-carrier-protien) reductase) was alighned against DHRS1 in 3D using Pymol. | |||
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[[DHRS1 Abstract| Abstract]] | [[DHRS1 Introduction| Introduction]] | [[DHRS1 Results| Results]] | [[DHRS1 Discussion| Discussion]] | | |||
[[DHRS1 Conclusion| Conclusion]] | [[DHRS1 Method| Method]] | [[DHRS1 References| References]] | |||
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[[Dehydrogenase/reductase (SDR family) member 1 | Back to Main Page]] | |||
Latest revision as of 02:01, 10 June 2008
BLAST
The protein sequence for the SDR family member 1 protein being investigated was downloaded from the PDB site, using the accession code 2qq5. This was then iteratively searched in blastp using an offline, non redundant copy of the database produced on the 28th of April 2008.
MULTIPLE SEQUENCE ALIGNMENT
The results from the blast search were then screened and a selection was of these results were used for a multiple sequence alignment using ClustalX. This result was boostrapped using 1000 simulations and these values checked and more sequences were added to improve the resolution of specific branches. A bootstrapped phylogram was produced.
TREE VIEW
The results from ClustalX were imported into treeview and a phylogenetic tree was produced, with bootstrapping values attached, and then split into bacteria and anamalia kingdoms.
STRUCTURAL ALIGNMENT
The protien sequence from PDB (2qq5) was aligned aginst other known sequences for structural similarity using the Dali web server. The structure of the most structurally related protien (Oxoacyl-(Acyl-carrier-protien) reductase) was alighned against DHRS1 in 3D using Pymol.
Abstract | Introduction | Results | Discussion |
Conclusion | Method | References
Back to Main Page
