Reshma Shetty/blog

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[http://openwetware.org/index.php?title=Reshma_Shetty/blog&action=history&feed=rss RSS]
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==5/10/2007==
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Today I wanted to find the number of operator sites for a given short sequence within the Escherichia coli.  The catch was that I also wanted to find operator sites with 1,2,3 or 4 mismatches to my specified operator site.  Here are some brief notes on how I figured out how to do this.
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Notes on finding the number of operator sites within the ''Escherichia coli'' genome.
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#Visit [http://colibase.bham.ac.uk/pattern/index.cgi?help=pattern&frame= coliBase's pattern search]
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#*For some reason it took multiple google searches and browsing to find this site!
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#Choose your genome, enter your sequence and the maximum number of mismatches you are willing to tolerate.
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#*Note that a 2 bp mismatch search will also find all 0 and 1 bp mismatches.  Also, the higher the number of mismatches, the longer it will take to run.
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#Copy and paste the search results to a text file (e.g. <code>filename.txt</code>).
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#*In my case, my operator was palindromic so I left out the second half of the search results that give the complementary strand hits (to avoid double counting).  Or save the whole file and divide your resulting numbers by two.
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#Use terminal or xterm on a Mac or Linux/Unix box.
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#Type <code>grep 4\ mismatches filename.txt</code> to list all 4 bp mismatches
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#Type <code>grep 4\ mismatches filename.txt | wc</code> to determine the count of all 4 bp mismatches.  The first number is the number of lines with the words "4 mismatches".  It is the count of the number of 4 bp mismatches in the genome.
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#*To find the number of 3 bp mismatches, type <code>grep 3\ mismatches filename.txt | wc</code> etc.
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Note that with 5 mismatches and a 14 bp sequence, it seemed to be truncating the results.  (I got fewer 2 bp mismatches in the 5 bp mismatch results than in the 4 bp mismatch results.) So be careful.
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See also [http://seq.yeastgenome.org/cgi-bin/PATMATCH/nph-patmatch Yeast pattern matching] and [http://campy.bham.ac.uk/about/index.cgi?help=about&frame= Campylobacter pattern matching].
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If anyone knows of a simpler way to do this, let me know.  It seems like there should be a program that just does this but I couldn't find it.
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==4/20/2007==
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With a lot of playing around by Vincent, Austin and I, we finally managed to find a reasonably straightforward way to make a google map on the wiki!  Check out [[OpenWetWare:Map]].  Please feel free to make your institution's call out box more interesting or fix coordinates etc.
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==3/23/2007 OpenWetWare institutions world tour==
==3/23/2007 OpenWetWare institutions world tour==
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<center> <script type="text/javascript" src="http://blip.tv/scripts/pokkariPlayer.js"></script><script type="text/javascript" src="http://blip.tv/syndication/write_player?skin=js&posts_id=182591&source=3&autoplay=true&file_type=flv&player_width=&player_height=500"></script><div id="blip_movie_content_182591"><a href="http://blip.tv/file/get/Openwetware-InstitutionWorldTour241.mov" onclick="play_blip_movie_182591(); return false;"><img src="http://blip.tv/file/get/Openwetware-InstitutionWorldTour241.mov.jpg" border="0" title="Click To Play" /></a><br /><a href="http://blip.tv/file/get/Openwetware-InstitutionWorldTour241.mov" onclick="play_blip_movie_182591(); return false;">Click To Play</a></div> </center><div class="blip_description">This movie is an around the world tour of institutions with labs on OpenWetWare (http://openwetware.org)<br /></div>
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<center> <script type="text/javascript" src="http://blip.tv/scripts/pokkariPlayer.js"></script><script type="text/javascript" src="http://blip.tv/syndication/write_player?skin=js&posts_id=182591&source=3&autoplay=true&file_type=flv&player_width=&player_height=500"></script><div id="blip_movie_content_182591"><a href="http://blip.tv/file/get/Openwetware-InstitutionWorldTour241.flv" onclick="play_blip_movie_182591(); return false;"><img src="http://blip.tv/file/get/Openwetware-InstitutionWorldTour241.flv.jpg" border="0" title="Click To Play" /></a><br /><a href="http://blip.tv/file/get/Openwetware-InstitutionWorldTour241.flv" onclick="play_blip_movie_182591(); return false;">Click To Play</a></div> </center><div class="blip_description">This movie is an around the world tour of institutions with labs on OpenWetWare (http://openwetware.org)<br /></div>
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Apologies to any institutions whose locations I got wrong.  I essentially just searched for institutions and found a location that looked approximately right.  If you'd like to fix your institution's location, here is the [[Media:OpenWetWare.kmz|kmz file]].  Or you can [[Talk:Reshma_Shetty/blog|give me new latitude and longitude coordinates]].  Also here are some notes on making [[Reshma Shetty/Google Earth tour videos|Google Earth tour videos]].
Apologies to any institutions whose locations I got wrong.  I essentially just searched for institutions and found a location that looked approximately right.  If you'd like to fix your institution's location, here is the [[Media:OpenWetWare.kmz|kmz file]].  Or you can [[Talk:Reshma_Shetty/blog|give me new latitude and longitude coordinates]].  Also here are some notes on making [[Reshma Shetty/Google Earth tour videos|Google Earth tour videos]].

Current revision

RSS

5/10/2007

Today I wanted to find the number of operator sites for a given short sequence within the Escherichia coli. The catch was that I also wanted to find operator sites with 1,2,3 or 4 mismatches to my specified operator site. Here are some brief notes on how I figured out how to do this.

Notes on finding the number of operator sites within the Escherichia coli genome.

  1. Visit coliBase's pattern search
    • For some reason it took multiple google searches and browsing to find this site!
  2. Choose your genome, enter your sequence and the maximum number of mismatches you are willing to tolerate.
    • Note that a 2 bp mismatch search will also find all 0 and 1 bp mismatches. Also, the higher the number of mismatches, the longer it will take to run.
  3. Copy and paste the search results to a text file (e.g. filename.txt).
    • In my case, my operator was palindromic so I left out the second half of the search results that give the complementary strand hits (to avoid double counting). Or save the whole file and divide your resulting numbers by two.
  4. Use terminal or xterm on a Mac or Linux/Unix box.
  5. Type grep 4\ mismatches filename.txt to list all 4 bp mismatches
  6. Type grep 4\ mismatches filename.txt | wc to determine the count of all 4 bp mismatches. The first number is the number of lines with the words "4 mismatches". It is the count of the number of 4 bp mismatches in the genome.
    • To find the number of 3 bp mismatches, type grep 3\ mismatches filename.txt | wc etc.

Note that with 5 mismatches and a 14 bp sequence, it seemed to be truncating the results. (I got fewer 2 bp mismatches in the 5 bp mismatch results than in the 4 bp mismatch results.) So be careful.

See also Yeast pattern matching and Campylobacter pattern matching.

If anyone knows of a simpler way to do this, let me know. It seems like there should be a program that just does this but I couldn't find it.

4/20/2007

With a lot of playing around by Vincent, Austin and I, we finally managed to find a reasonably straightforward way to make a google map on the wiki! Check out OpenWetWare:Map. Please feel free to make your institution's call out box more interesting or fix coordinates etc.

3/23/2007 OpenWetWare institutions world tour

For no real reason, I started playing around with Google Earth and made the following world tour of institutions with labs on OpenWetWare. (Equal credit goes to Austin and Mac for helping me actually generate the video!) Note that this video is about 10 mins long.


This movie is an around the world tour of institutions with labs on OpenWetWare (http://openwetware.org)


Apologies to any institutions whose locations I got wrong. I essentially just searched for institutions and found a location that looked approximately right. If you'd like to fix your institution's location, here is the kmz file. Or you can give me new latitude and longitude coordinates. Also here are some notes on making Google Earth tour videos.

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