Team:The University of Alberta/16 May 2008

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<li>http://www.expasy.ch/ - '''ExPASy Proteomics Server''': This site has tons of tools that we'll probably never use, but there are still a few useful things:<ul>
<li>http://www.expasy.ch/ - '''ExPASy Proteomics Server''': This site has tons of tools that we'll probably never use, but there are still a few useful things:<ul>
<li> '''Translate'''(http://www.expasy.ch/tools/dna.html) This will let you translate your cDNA sequence into an amino acid sequence at the click of a button!
<li> '''Translate'''(http://www.expasy.ch/tools/dna.html) This will let you translate your cDNA sequence into an amino acid sequence at the click of a button!
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<li> '''ProSite'' and '''ScanProSite''' (http://www.expasy.ch/prosite/) These let you search your amino acid sequence to check for domains, modification sites, etc. Probably not useful but it does have a tool that allows you to make some neat schematic diagrams of genes/proteins like the one below:
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<li> '''ProSite and''' '''ScanProSite''' (http://www.expasy.ch/prosite/) These let you search your amino acid sequence to check for domains, modification sites, etc. Probably not useful but it does have a tool that allows you to make some neat schematic diagrams of genes/proteins like the one below:
[[Image:examplediagram.png]]
[[Image:examplediagram.png]]

Revision as of 20:26, 16 May 2008

To Do

Plant Seminar @ 4:00pm

In the Lab

Chris

  • I finished sequencing the thiolase gene again; the samples need to be run up to the MBSU
  • Jason and I designed the BioBrick for PIF3; I spent some time trying to do codon optimization for E.Coli I downloaded a program onto one of the computers in the back of the lab for optimizing the BioBricks but it doesnt seem to work very well; use this[http://genomes.urv.es/OPTIMIZER] website instead if you want to work on codon optimization.
  • The PIF3 BioBrick doesn't have a His-tag added to it. Can't forget to do that before we get them synthesized.


If anyone wants to work on building BioBricks, these sites are a good help:
  • http://www.arabidopsis.org - The Arabidposis Information Resource (TAIR): This site will help you find the sequences for the genes and proteins that we want from Arabidopsis. It's best if you use cDNA sequences because these already have the introns spliced from them!
  • http://www.ebi.ac.uk/Tools/clustalw2/index.html - ClustalW: This site is great for aligning two DNA or protein sequences. This makes it super easy to check to make sure your edited/optimized sequences still code from the same thing as the reference sequences from TAIR.
  • http://www.expasy.ch/ - ExPASy Proteomics Server: This site has tons of tools that we'll probably never use, but there are still a few useful things:
    • Translate(http://www.expasy.ch/tools/dna.html) This will let you translate your cDNA sequence into an amino acid sequence at the click of a button!
    • ProSite and ScanProSite (http://www.expasy.ch/prosite/) These let you search your amino acid sequence to check for domains, modification sites, etc. Probably not useful but it does have a tool that allows you to make some neat schematic diagrams of genes/proteins like the one below: Examplediagram.png
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