Difference between revisions of "BASIC PROTOCOL 6: SEARCHING FOR GENE PRODUCTS WITH PARTICULAR SEQUENCE MOTIFS"

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(New page: One way to identify all ''C. elegans'' proteins sharing a given PFAM or InterPro motif is to check that motif's WormBase entry. One advantage of such searches is that hypertext links are g...)
 
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1. From the front page, enter a term for the desired motif, such as "ribonucleoprotein", select "Protein Family or Motif" from the pull-down menu (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png), click Search, and study the results.
 
1. From the front page, enter a term for the desired motif, such as "ribonucleoprotein", select "Protein Family or Motif" from the pull-down menu (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png), click Search, and study the results.
  
[[Image:Fig_1_8_07.png]]
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http://www.wormbase.org/wiki/images/Fig_1_8_07.png
  
 
Click on the hyperlinked motifs and examine them individually to see which are most useful.
 
Click on the hyperlinked motifs and examine them individually to see which are most useful.
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''An example of a motif found by searching for'' ribonucleoprotein ''is the InterPro motif IPR001163, "Like-Sm ribonucleoprotein, core." The motif has 17 associated proteins; in cases where a motif's gene has a classical three-letter name, this is shown.''
 
''An example of a motif found by searching for'' ribonucleoprotein ''is the InterPro motif IPR001163, "Like-Sm ribonucleoprotein, core." The motif has 17 associated proteins; in cases where a motif's gene has a classical three-letter name, this is shown.''
  
[[Image:Fig_1_8_08.png]]
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http://www.wormbase.org/wiki/images/Fig_1_8_08.png

Revision as of 21:21, 23 September 2007

One way to identify all C. elegans proteins sharing a given PFAM or InterPro motif is to check that motif's WormBase entry. One advantage of such searches is that hypertext links are given for each motif to a short description of its biological properties (if any; many motifs are evolutionarily conserved but functionally uncharacterized).

Necessary Resources

Hardware

   A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)

Software

   Web browser such as Internet Explorer (http://www.microsoft.com) or Mozilla (http://www.mozilla.org/firefox)

1. From the front page, enter a term for the desired motif, such as "ribonucleoprotein", select "Protein Family or Motif" from the pull-down menu (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png), click Search, and study the results.

Fig_1_8_07.png

Click on the hyperlinked motifs and examine them individually to see which are most useful.

2. Alternatively, pick a gene whose protein product is known to be in the class of interest. Find its Gene page by a standard search (see Basic Protocol 3). Click from there to its Protein page(s) and check for motifs. (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_06.png)

3. Using either method, if one or more motifs are found, click on them to see whether they have other proteins associated with them.

An example of a motif found by searching for ribonucleoprotein is the InterPro motif IPR001163, "Like-Sm ribonucleoprotein, core." The motif has 17 associated proteins; in cases where a motif's gene has a classical three-letter name, this is shown.

Fig_1_8_08.png