http://openwetware.org/index.php?title=Tregwiki:Main_Page&feed=atom&action=history 2013-05-21T02:37:59Z Revision history for this page on the wiki MediaWiki 1.13.2 http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=189234&oldid=prev 2008-03-04T15:06:09Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:06, 4 March 2008</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 21:</td> <td colspan="2" class="diff-lineno">Line 21:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** [[Tools for matrices|Visualize and compare your results]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** [[Tools for matrices|Visualize and compare your results]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:Scanning promotors|Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:Scanning promotors|Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics|Calculate statistics]] of DNA-words or <del class="diffchange diffchange-inline">[</del>[[Tregwiki:Discover motif combinations|Discover motif combinations]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics|Calculate statistics]] of DNA-words or [[Tregwiki:Discover motif combinations|Discover motif combinations]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Tregwiki:Recent bibliography|Recent papers on regulation]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Tregwiki:Recent bibliography|Recent papers on regulation]]</div></td></tr> <!-- diff generator: internal 2013-05-21 02:37:59 --> </table>

Torsten Waldminghaus http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=189217&oldid=prev 2008-03-04T10:57:22Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 10:57, 4 March 2008</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 19:</td> <td colspan="2" class="diff-lineno">Line 19:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Look up: In databases of known [[Tregwiki:Collected regulatory elements|Collected regulatory elements]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Look up: In databases of known [[Tregwiki:Collected regulatory elements|Collected regulatory elements]]</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">** [[Tools for matrices|Visualize and compare your results]]</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:Scanning promotors|Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:Scanning promotors|Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics|Calculate statistics]] of DNA-words or [[[Tregwiki:Discover motif combinations|Discover motif combinations]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics|Calculate statistics]] of DNA-words or [[[Tregwiki:Discover motif combinations|Discover motif combinations]]</div></td></tr> <!-- diff generator: internal 2013-05-21 02:37:59 --> </table>

Maximilianh http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=174556&oldid=prev 2007-12-12T11:42:39Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:42, 12 December 2007</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Welcome to '''[[Tregwiki:Max|<del class="diffchange diffchange-inline">Msx</del>'s]] Wiki on Transcriptional Regulation'''. ([[Tregwiki:Max|who's max?]])</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Welcome to '''[[Tregwiki:Max|<ins class="diffchange diffchange-inline">Max</ins>'s]] Wiki on Transcriptional Regulation'''. ([[Tregwiki:Max|who's max?]])</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td></tr> <!-- diff generator: internal 2013-05-21 02:37:59 --> </table>

Honza83 http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=174460&oldid=prev 2007-12-11T20:07:34Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 20:07, 11 December 2007</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Welcome to '''[[Tregwiki:Max<del class="diffchange diffchange-inline">]]</del>'s Wiki on Transcriptional Regulation'''. ([[Tregwiki:Max|who's max?]])</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Welcome to '''[[Tregwiki:Max<ins class="diffchange diffchange-inline">|Msx</ins>'s<ins class="diffchange diffchange-inline">]] </ins>Wiki on Transcriptional Regulation'''. ([[Tregwiki:Max|who's max?]])</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>I am collecting links related to bioinformatics and binding site prediction ([[Tregwiki:Why is this a difficult problem]]?).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>I am collecting links related to bioinformatics and binding site prediction ([[Tregwiki:<ins class="diffchange diffchange-inline">Why is this a difficult problem|</ins>Why is this a difficult problem]]?).</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>There are usually many different solutions for every problem in bioinformatics. This list might shorten your mileage when choosing an appropriate one.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>There are usually many different solutions for every problem in bioinformatics. This list might shorten your mileage when choosing an appropriate one.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Promotors/Enhancers/Regulatory Regions:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Promotors/Enhancers/Regulatory Regions:</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Assemble: [[Tregwiki:Assembling promotors from trace databases]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Assemble: [[Tregwiki:<ins class="diffchange diffchange-inline">Assembling promotors from trace databases|</ins>Assembling promotors from trace databases]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Narrow down: [[Tregwiki:Predict promotor regions|Predict promotors/enhancers]] in silico</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Narrow down: [[Tregwiki:Predict promotor regions|Predict promotors/enhancers]] in silico</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Check if ncRNA: [[Tregwiki:Folding Alignments]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Check if ncRNA: [[Tregwiki:<ins class="diffchange diffchange-inline">Folding Alignments|</ins>Folding Alignments]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Find Orthologs: [[Tregwiki:Finding interspecies-orthologs]] for multiple alignments</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Find Orthologs: [[Tregwiki:<ins class="diffchange diffchange-inline">Finding interspecies-orthologs|</ins>Finding interspecies-orthologs]] for multiple alignments</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Sort by Function: [[Tregwiki:Gene Ontology Tools]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Sort by Function: [[Tregwiki:<ins class="diffchange diffchange-inline">Gene Ontology Tools|</ins>Gene Ontology Tools]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Download: [[Tregwiki:Downloading promotors]] aka upstream regions ''en masse''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Download: [[Tregwiki:<ins class="diffchange diffchange-inline">Downloading promotors|</ins>Downloading promotors]] aka upstream regions ''en masse''</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki:Whole-Genome Alignments]] to [[Tregwiki:FindConservedNoncoding|delineate conserved non-coding]] elements</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki:<ins class="diffchange diffchange-inline">Whole-Genome Alignments|</ins>Whole-Genome Alignments]] to [[Tregwiki:FindConservedNoncoding|delineate conserved non-coding]] elements</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Visualize [[Tregwiki:Multi-sequence visualization of features]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Visualize [[Tregwiki:<ins class="diffchange diffchange-inline">Multi-sequence visualization of features|</ins>Multi-sequence visualization of features]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Altogether: [[Tregwiki:Enhancerprediction|Prediction of clusters of sites]] with optional conservation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Altogether: [[Tregwiki:Enhancerprediction|Prediction of clusters of sites]] with optional conservation</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Look up: In databases of known [[Tregwiki:Collected regulatory elements]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Look up: In databases of known [[Tregwiki:<ins class="diffchange diffchange-inline">Collected regulatory elements|</ins>Collected regulatory elements]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:<ins class="diffchange diffchange-inline">Scanning promotors|</ins>Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics]] of DNA-words or [[Tregwiki:Discover motif combinations]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:<ins class="diffchange diffchange-inline">Calculate statistics|</ins>Calculate statistics]] of DNA-words or <ins class="diffchange diffchange-inline">[</ins>[[Tregwiki:<ins class="diffchange diffchange-inline">Discover motif combinations|</ins>Discover motif combinations]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Tregwiki:Recent bibliography|Recent papers on regulation]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Tregwiki:Recent bibliography|Recent papers on regulation]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Transcription Factors: (new)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Transcription Factors: (new)</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Tregwiki:Lists of Factors]] by similarity</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[Tregwiki:<ins class="diffchange diffchange-inline">Lists of Factors|</ins>Lists of Factors]] by similarity</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[Tregwiki:Meta-Websites]] that integrate promotor download, motif matching/discovery</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* [[Tregwiki:<ins class="diffchange diffchange-inline">Meta-Websites|</ins>Meta-Websites]] that integrate promotor download, motif matching/discovery</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* General topics link collection:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* General topics link collection:</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Tregwiki:Libraries for Programmers]] working on transcriptional regulation</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[Tregwiki:<ins class="diffchange diffchange-inline">Libraries for Programmers|</ins>Libraries for Programmers]] working on transcriptional regulation</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Tregwiki:People working on transcription regulation]] (please add yourself here!)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[Tregwiki:<ins class="diffchange diffchange-inline">People working on transcription regulation|</ins>People working on transcription regulation]] (please add yourself here!)</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Tregwiki:General websites]] for transcriptional regulation</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[Tregwiki:<ins class="diffchange diffchange-inline">General websites|</ins>General websites]] for transcriptional regulation</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Tregwiki:The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[Tregwiki:<ins class="diffchange diffchange-inline">The structure of DNA|</ins>The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Tregwiki:In-situ databases]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[Tregwiki:<ins class="diffchange diffchange-inline">In-situ databases|</ins>In-situ databases]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Tregwiki:Conferences]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[Tregwiki:<ins class="diffchange diffchange-inline">Conferences|</ins>Conferences]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** <del class="diffchange diffchange-inline">The </del>[<del class="diffchange diffchange-inline">[Tregwiki</del>:Jim Kent Source Tree<del class="diffchange diffchange-inline">]</del>]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [<ins class="diffchange diffchange-inline">http</ins>:<ins class="diffchange diffchange-inline">//genomewiki.cse.ucsc.edu/index.php/The_source_tree The </ins>Jim Kent Source Tree]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>There are a couple of [[Tregwiki:Similar link collections]] on the web.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>There are a couple of [[Tregwiki:<ins class="diffchange diffchange-inline">Similar link collections|</ins>Similar link collections]] on the web.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Sometimes [[Tregwiki:Gene Ontology related]] tools are useful when working with transcriptional regulation.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Sometimes [[Tregwiki:<ins class="diffchange diffchange-inline">Gene Ontology related|</ins>Gene Ontology related]] tools are useful when working with transcriptional regulation.</div></td></tr> <!-- diff generator: internal 2013-05-21 02:37:59 --> </table>

Bill Flanagan http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=174456&oldid=prev 2007-12-11T19:58:09Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 19:58, 11 December 2007</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Welcome to '''[[Tregwiki:Max]]'s Wiki on Transcriptional Regulation'''. ([[Tregwiki:<del class="diffchange diffchange-inline">max</del>|who's max?]])</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Welcome to '''[[Tregwiki:Max]]'s Wiki on Transcriptional Regulation'''. ([[Tregwiki:<ins class="diffchange diffchange-inline">Max</ins>|who's max?]])</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 13:</td> <td colspan="2" class="diff-lineno">Line 13:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Sort by Function: [[Tregwiki:Gene Ontology Tools]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Sort by Function: [[Tregwiki:Gene Ontology Tools]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Download: [[Tregwiki:Downloading promotors]] aka upstream regions ''en masse''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Download: [[Tregwiki:Downloading promotors]] aka upstream regions ''en masse''</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki:Whole-Genome Alignments]] to [[FindConservedNoncoding|delineate conserved non-coding]] elements</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki:Whole-Genome Alignments]] to [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>FindConservedNoncoding|delineate conserved non-coding]] elements</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Visualize [[Tregwiki:Multi-sequence visualization of features]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Visualize [[Tregwiki:Multi-sequence visualization of features]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Altogether: [[Tregwiki:Enhancerprediction|Prediction of clusters of sites]] with optional conservation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Altogether: [[Tregwiki:Enhancerprediction|Prediction of clusters of sites]] with optional conservation</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Look up: In databases of known [[Tregwiki:<del class="diffchange diffchange-inline">collected </del>regulatory elements]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Look up: In databases of known [[Tregwiki:<ins class="diffchange diffchange-inline">Collected </ins>regulatory elements]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Scan: [[Tregwiki:Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Predict: [<del class="diffchange diffchange-inline">Tregwiki:</del>http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[<del class="diffchange diffchange-inline">calculate </del>statistics]] of DNA-words or [[Tregwiki:<del class="diffchange diffchange-inline">discover </del>motif combinations]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[<ins class="diffchange diffchange-inline">Tregwiki:Calculate </ins>statistics]] of DNA-words or [[Tregwiki:<ins class="diffchange diffchange-inline">Discover </ins>motif combinations]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[Tregwiki:<del class="diffchange diffchange-inline">recent </del>bibliography|Recent papers on regulation]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* [[Tregwiki:<ins class="diffchange diffchange-inline">Recent </ins>bibliography|Recent papers on regulation]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Transcription Factors: (new)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Transcription Factors: (new)</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 30:</td> <td colspan="2" class="diff-lineno">Line 30:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* General topics link collection:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* General topics link collection:</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Libraries for Programmers]] working on transcriptional regulation</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Libraries for Programmers]] working on transcriptional regulation</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[People working on transcription regulation]] (please add yourself here!)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>People working on transcription regulation]] (please add yourself here!)</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[General websites]] for transcriptional regulation</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>General websites]] for transcriptional regulation</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[In-situ databases]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>In-situ databases]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Conferences]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Conferences]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** The [[Jim Kent Source Tree]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** The [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Jim Kent Source Tree]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>There are a couple of [[<del class="diffchange diffchange-inline">similar </del>link collections]] on the web.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>There are a couple of [[<ins class="diffchange diffchange-inline">Tregwiki:Similar </ins>link collections]] on the web.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Sometimes [[Gene Ontology related]] tools are useful when working with transcriptional regulation.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Sometimes [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Gene Ontology related]] tools are useful when working with transcriptional regulation.</div></td></tr> <!-- diff generator: internal 2013-05-21 02:37:59 --> </table>

Bill Flanagan http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=174453&oldid=prev 2007-12-11T19:49:37Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 19:49, 11 December 2007</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Welcome to '''[[Max]]'s Wiki on Transcriptional Regulation'''. ([[max|who's max?]])</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Welcome to '''[[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Max]]'s Wiki on Transcriptional Regulation'''. ([[<ins class="diffchange diffchange-inline">Tregwiki:</ins>max|who's max?]])</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>I am collecting links related to bioinformatics and binding site prediction ([[Why is this a difficult problem]]?).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>I am collecting links related to bioinformatics and binding site prediction ([[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Why is this a difficult problem]]?).</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>There are usually many different solutions for every problem in bioinformatics. This list might shorten your mileage when choosing an appropriate one.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>There are usually many different solutions for every problem in bioinformatics. This list might shorten your mileage when choosing an appropriate one.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Promotors/Enhancers/Regulatory Regions:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Promotors/Enhancers/Regulatory Regions:</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Assemble: [[Assembling promotors from trace databases]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Assemble: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Assembling promotors from trace databases]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Narrow down: [[Predict promotor regions|Predict promotors/enhancers]] in silico</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Narrow down: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Predict promotor regions|Predict promotors/enhancers]] in silico</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Check if ncRNA: [[Folding Alignments]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Check if ncRNA: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Folding Alignments]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Find Orthologs: [[Finding interspecies-orthologs]] for multiple alignments</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Find Orthologs: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Finding interspecies-orthologs]] for multiple alignments</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Sort by Function: [[Gene Ontology Tools]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Sort by Function: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Gene Ontology Tools]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Download: [[Downloading promotors]] aka upstream regions ''en masse''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Download: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Downloading promotors]] aka upstream regions ''en masse''</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Align: [[Aligning promotors|Align non-coding sequences]] or use [[Whole-Genome Alignments]] to [[FindConservedNoncoding|delineate conserved non-coding]] elements</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Align: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Aligning promotors|Align non-coding sequences]] or use [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Whole-Genome Alignments]] to [[FindConservedNoncoding|delineate conserved non-coding]] elements</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Visualize [[Multi-sequence visualization of features]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Visualize [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Multi-sequence visualization of features]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Altogether: [[Enhancerprediction|Prediction of clusters of sites]] with optional conservation</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Altogether: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Enhancerprediction|Prediction of clusters of sites]] with optional conservation</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Binding sites:</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Look up: In databases of known [[collected regulatory elements]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Look up: In databases of known [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>collected regulatory elements]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Scan: [[Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Scan: [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Scanning promotors]] or enhancers for binding site matrices or consensus sequences</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[calculate statistics]] of DNA-words or [[discover motif combinations]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Predict: [<ins class="diffchange diffchange-inline">Tregwiki:</ins>http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[calculate statistics]] of DNA-words or [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>discover motif combinations]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[recent bibliography|Recent papers on regulation]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>recent bibliography|Recent papers on regulation]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Transcription Factors: (new)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Transcription Factors: (new)</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[Lists of Factors]] by similarity</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Lists of Factors]] by similarity</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[Meta-Websites]] that integrate promotor download, motif matching/discovery</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* [[<ins class="diffchange diffchange-inline">Tregwiki:</ins>Meta-Websites]] that integrate promotor download, motif matching/discovery</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td></tr> <!-- diff generator: internal 2013-05-21 02:38:00 --> </table>

Bill Flanagan http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=174448&oldid=prev 2007-12-11T19:41:07Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 19:41, 11 December 2007</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 47:</td> <td colspan="2" class="diff-lineno">Line 47:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>There are a couple of [[similar link collections]] on the web.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>There are a couple of [[similar link collections]] on the web.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sometimes [[Gene Ontology related]] tools are useful when working with transcriptional regulation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Sometimes [[Gene Ontology related]] tools are useful when working with transcriptional regulation.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">maximilianh--at--gmail.com</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> &lt;br&gt;&lt;br&gt;&lt;u style=&quot;display:none;&quot;&gt;[http://jira.opensymphony.com/secure/attachment/12901/creampie.html Anal Creampie] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Creampie Surprise] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Creampie Galleries] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Creampie Pussies] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Teen Creampie]</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html Drunk Sex Orgy] [http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html Party Hardcore] [http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html College Wild Parties] [http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html Drunk Party]</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Gay cowboys] [http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Huge gay cock] [http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Big gay dick] [http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Black gay dick]</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Black Seducer] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Boys Collection] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Boys Wedding] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Black Machines] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Gay Lessons]</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Mature Porn] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Mature Lessons] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html World Mature] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Mature Debutants] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Banged Moms]</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale sex] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale galleries] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale movies] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Black shemales] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale porn]</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleeping Sex] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleep Assault] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleeping Bitch] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleeping Bitches] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Night Invasion]</del></div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[http://jira.opensymphony.com/secure/attachment/12908/stockings.html Stocking tease] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Black stockings] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Stocking mania] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Silk stockings] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Stocking sex] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Nylon stockings]&lt;/u&gt;</del></div></td><td colspan="2">&nbsp;</td></tr> <!-- diff generator: internal 2013-05-21 02:38:00 --> </table>

Jason R. Kelly http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=173833&oldid=prev 2007-12-09T22:28:35Z

<p>1 revision(s)</p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:28, 9 December 2007</td> </tr> <!-- diff generator: internal 2013-05-19 10:55:55 --> <!-- diff cache key owwdb:diff:version:1.11a:oldid:173832:newid:173833 --> </table>

Bill Flanagan http://openwetware.org/index.php?title=Tregwiki:Main_Page&diff=173832&oldid=prev 2007-11-29T21:40:27Z

<p>despam</p> <p><b>New page</b></p><div>Welcome to '''[[Max]]'s Wiki on Transcriptional Regulation'''. ([[max|who's max?]])<br /> <br /> ''&quot;Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all.&quot; (Thomas Carlyle)''<br /> <br /> I am collecting links related to bioinformatics and binding site prediction ([[Why is this a difficult problem]]?).<br /> There are usually many different solutions for every problem in bioinformatics. This list might shorten your mileage when choosing an appropriate one.<br /> <br /> * Promotors/Enhancers/Regulatory Regions:<br /> ** Assemble: [[Assembling promotors from trace databases]]<br /> ** Narrow down: [[Predict promotor regions|Predict promotors/enhancers]] in silico<br /> ** Check if ncRNA: [[Folding Alignments]]<br /> ** Find Orthologs: [[Finding interspecies-orthologs]] for multiple alignments<br /> ** Sort by Function: [[Gene Ontology Tools]]<br /> ** Download: [[Downloading promotors]] aka upstream regions ''en masse''<br /> ** Align: [[Aligning promotors|Align non-coding sequences]] or use [[Whole-Genome Alignments]] to [[FindConservedNoncoding|delineate conserved non-coding]] elements<br /> ** Visualize [[Multi-sequence visualization of features]]<br /> ** Altogether: [[Enhancerprediction|Prediction of clusters of sites]] with optional conservation<br /> <br /> *Binding sites:<br /> ** Look up: In databases of known [[collected regulatory elements]]<br /> ** Scan: [[Scanning promotors]] or enhancers for binding site matrices or consensus sequences<br /> ** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[calculate statistics]] of DNA-words or [[discover motif combinations]]<br /> <br /> * [[recent bibliography|Recent papers on regulation]]<br /> <br /> *Transcription Factors: (new)<br /> ** [[Lists of Factors]] by similarity<br /> <br /> * [[Meta-Websites]] that integrate promotor download, motif matching/discovery<br /> <br /> ----<br /> <br /> <br /> <br /> <br /> <br /> <br /> * General topics link collection:<br /> ** [[Libraries for Programmers]] working on transcriptional regulation<br /> ** [[People working on transcription regulation]] (please add yourself here!)<br /> ** [[General websites]] for transcriptional regulation<br /> ** [[The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here.<br /> ** [[In-situ databases]]<br /> ** [[Conferences]]<br /> ** The [[Jim Kent Source Tree]]<br /> <br /> There are a couple of [[similar link collections]] on the web.<br /> Sometimes [[Gene Ontology related]] tools are useful when working with transcriptional regulation.<br /> <br /> <br /> maximilianh--at--gmail.com<br /> &lt;br&gt;&lt;br&gt;&lt;u style=&quot;display:none;&quot;&gt;[http://jira.opensymphony.com/secure/attachment/12901/creampie.html Anal Creampie] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Creampie Surprise] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Creampie Galleries] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Creampie Pussies] [http://jira.opensymphony.com/secure/attachment/12901/creampie.html Teen Creampie]<br /> [http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html Drunk Sex Orgy] [http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html Party Hardcore] [http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html College Wild Parties] [http://jira.opensymphony.com/secure/attachment/12902/drunksexorgy.html Drunk Party]<br /> [http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Gay cowboys] [http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Huge gay cock] [http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Big gay dick] [http://jira.opensymphony.com/secure/attachment/12903/gaycowboys.html Black gay dick]<br /> [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Black Seducer] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Boys Collection] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Boys Wedding] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Black Machines] [http://jira.opensymphony.com/secure/attachment/12904/gaylessons.html Gay Lessons]<br /> [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Mature Porn] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Mature Lessons] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html World Mature] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Mature Debutants] [http://jira.opensymphony.com/secure/attachment/12905/matureporn.html Banged Moms]<br /> [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale sex] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale galleries] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale movies] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Black shemales] [http://jira.opensymphony.com/secure/attachment/12906/shemaleporn.html Shemale porn]<br /> [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleeping Sex] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleep Assault] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleeping Bitch] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Sleeping Bitches] [http://jira.opensymphony.com/secure/attachment/12907/sleepingsex.html Night Invasion]<br /> [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Stocking tease] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Black stockings] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Stocking mania] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Silk stockings] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Stocking sex] [http://jira.opensymphony.com/secure/attachment/12908/stockings.html Nylon stockings]&lt;/u&gt;</div>

Admin