Reshma Shetty/blog - Revision history

Reshma P. Shetty at 18:50, 10 May 2007

Reshma P. Shetty — Thu, 10 May 2007 18:50:26 GMT

←Older revision		Revision as of 18:50, 10 May 2007
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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.		#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.
	#*To find the number of 3 bp mismatches, type <code>grep 3\ mismatches filename.txt \| wc</code> etc.		#*To find the number of 3 bp mismatches, type <code>grep 3\ mismatches filename.txt \| wc</code> 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 [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].		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].

-	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 it ~~took quite a bit of googling to figure out this ugly approach~~.	+	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==		==4/20/2007==

Reshma P. Shetty: /* 5/10/2007 */

Reshma P. Shetty — Thu, 10 May 2007 18:37:27 GMT

5/10/2007

←Older revision		Revision as of 18:37, 10 May 2007
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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].		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].

-	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 it took quite a bit of googling to ~~find~~ this.	+	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 it took quite a bit of googling to figure out this ugly approach.

	==4/20/2007==		==4/20/2007==

Reshma P. Shetty at 18:36, 10 May 2007

Reshma P. Shetty — Thu, 10 May 2007 18:36:42 GMT

←Older revision		Revision as of 18:36, 10 May 2007
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	[http://openwetware.org/index.php?title=Reshma_Shetty/blog&action=history&feed=rss RSS]		[http://openwetware.org/index.php?title=Reshma_Shetty/blog&action=history&feed=rss 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.
		+
		+	#Visit [http://colibase.bham.ac.uk/pattern/index.cgi?help=pattern&frame= coliBase's pattern search]
		+	#*For some reason it took multiple google searches and browsing to find this site!
		+	#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.
		+	#Copy and paste the search results to a text file (e.g. <code>filename.txt</code>).
		+	#*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.
		+	#Use terminal or xterm on a Mac or Linux/Unix box.
		+	#Type <code>grep 4\ mismatches filename.txt</code> to list all 4 bp mismatches
		+	#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.
		+	#*To find the number of 3 bp mismatches, type <code>grep 3\ mismatches filename.txt \| wc</code> etc.
		+
		+	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].
		+
		+	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 it took quite a bit of googling to find this.

	==4/20/2007==		==4/20/2007==

Reshma P. Shetty at 14:56, 20 April 2007

Reshma P. Shetty — Fri, 20 Apr 2007 14:56:27 GMT

←Older revision		Revision as of 14:56, 20 April 2007
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	[http://openwetware.org/index.php?title=Reshma_Shetty/blog&action=history&feed=rss RSS]		[http://openwetware.org/index.php?title=Reshma_Shetty/blog&action=history&feed=rss RSS]
		+
		+	==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==		==3/23/2007 OpenWetWare institutions world tour==

Reshma P. Shetty at 23:06, 4 April 2007

Reshma P. Shetty — Wed, 04 Apr 2007 23:06:02 GMT

←Older revision		Revision as of 23:06, 4 April 2007
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		+	[http://openwetware.org/index.php?title=Reshma_Shetty/blog&action=history&feed=rss RSS]
		+
	==3/23/2007 OpenWetWare institutions world tour==		==3/23/2007 OpenWetWare institutions world tour==

Reshma P. Shetty at 15:31, 24 March 2007

Reshma P. Shetty — Sat, 24 Mar 2007 15:31:17 GMT

←Older revision		Revision as of 15:31, 24 March 2007
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	<html>		<html>
-	<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>	+	<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>
	</html>		</html>


	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]].

Reshma P. Shetty at 01:20, 24 March 2007

Reshma P. Shetty — Sat, 24 Mar 2007 01:20:46 GMT

←Older revision		Revision as of 01:20, 24 March 2007
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	</html>		</html>

-	~~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]].

Reshma P. Shetty at 01:07, 24 March 2007

Reshma P. Shetty — Sat, 24 Mar 2007 01:07:31 GMT

←Older revision		Revision as of 01:07, 24 March 2007
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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>		<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>
	</html>		</html>
		+
		+	Some notes on making [[Reshma Shetty/Google Earth tour videos\|Google Earth tour videos]].

Reshma P. Shetty: New page: ==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...

Reshma P. Shetty — Sat, 24 Mar 2007 00:54:08 GMT

New page: ==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...

New page

==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.

<html>
<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>
</html>