Difference between revisions of "CSC334 Lab2"
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| + | <meta name="keywords" content="computer science, bioinformatics, DNA, CSC334, Lab" /> | ||
| + | <meta name="description" content="DNA Sequence Logo Lab" /> | ||
| + | <meta name="title" content="Bioinformatics Lab" /> | ||
| + | <meta name="abstract" content="DNA Sequence Logo" /> | ||
| + | <meta name="author" content="thiebaut at cs.smith.edu" /> | ||
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| + | [[Csc334_Labs | Back to CSC334 Lab Page]] | ||
| + | <hr> | ||
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=Retrieving Protein sequences from ExPASy= | =Retrieving Protein sequences from ExPASy= | ||
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==Methodology== | ==Methodology== | ||
| − | * Point your browser to [http://www.expasy.org/sprot/ www.expasy.org/sprot/] and enter DUT_ECOLI in the search bar: | + | * Point your browser to [http://www.expasy.org/sprot/ www.expasy.org/sprot/] and enter''' DUT_ECOLI''' in the search bar and click on '''Go''': |
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[[Image:CSC334_Lab2_1.png | thumb | 300 px | frame | Figure 1]] | [[Image:CSC334_Lab2_1.png | thumb | 300 px | frame | Figure 1]] | ||
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| + | * The '''Accession Number''' of the protein found is '''P06968'''. Its name in the Swiss-Prot database is DUT_ECOLI, but it is also known as EC 3.6.1.23, or dUTPase, or dUTP pyrophospatase. | ||
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| + | * Find the '''Sequence Information''' at the bottom of the page, and select '''P06968 in FASTA''' format for the display. You should get something like this: | ||
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| + | >sp|P06968|DUT_ECOLI Deoxyuridine 5'-triphosphate nucleotidohydrolase OS=Escherichia coli (strain K12) GN=dut PE=1 SV=1 | ||
| + | MKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIAD | ||
| + | PSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMI | ||
| + | FVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ | ||
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| + | <hr> | ||
| + | [[Csc334_Labs | Back to CSC334 Lab Page]] | ||
| + | <br /> | ||
| + | © D. Thiebaut 2008 | ||
Latest revision as of 18:11, 4 August 2008
<meta name="keywords" content="computer science, bioinformatics, DNA, CSC334, Lab" /> <meta name="description" content="DNA Sequence Logo Lab" /> <meta name="title" content="Bioinformatics Lab" /> <meta name="abstract" content="DNA Sequence Logo" /> <meta name="author" content="thiebaut at cs.smith.edu" />
Retrieving Protein sequences from ExPASy
ExPASy is a database of proteins created by a pioneer of bioinformatics: Amos Bairoch
Methodology
- Point your browser to www.expasy.org/sprot/ and enter DUT_ECOLI in the search bar and click on Go:
- The Accession Number of the protein found is P06968. Its name in the Swiss-Prot database is DUT_ECOLI, but it is also known as EC 3.6.1.23, or dUTPase, or dUTP pyrophospatase.
- Find the Sequence Information at the bottom of the page, and select P06968 in FASTA format for the display. You should get something like this:
>sp|P06968|DUT_ECOLI Deoxyuridine 5'-triphosphate nucleotidohydrolase OS=Escherichia coli (strain K12) GN=dut PE=1 SV=1 MKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIAD PSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMI FVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ
Back to CSC334 Lab Page
© D. Thiebaut 2008
