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Revision: 1.1.1.1 (vendor branch)
Committed: Mon Aug 23 19:36:28 2004 UTC (15 years, 7 months ago) by malay
Branch: MAIN
CVS Tags: HEAD, HEAD
Changes since 1.1: +0 -0 lines
Log Message:
First import

Line File contents
1 <html>
2
3 <head>
4 <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
5 <meta name="author" content="Dr Malay K Basu">
6 <!--Do not edit this tag-->
7 <!--Section #1 code goes here-->
8 <!--included_programs="primer3,codehop"-->
9 <!--Section #1 code goes here-->
10 <title>SeWeR: PCR</title>
11
12 <script language="JavaScript" src="scripts/browser.js"></script>
13 <script language="JavaScript1.2" src="scripts/sewer.js"></script>
14
15 <script language="JavaScript1.2">
16 function init(){
17 if(isNS6){
18 document.all=document.getElementsByTagName("*");
19 }
20 program=new Array();
21 program[0]=new ProgramConstructor("primer3","http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi","http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www_results.cgi","http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www_help.cgi","SEQUENCE","post","application/x-www-form-urlencoded");
22 program[1]=new ProgramConstructor("codehop","http://bioinformatics.weizmann.ac.il/blocks/codehop.html","http://bioinformatics.weizmann.ac.il/blocks-bin/codehop.pl","http://bioinformatics.weizmann.ac.il/blocks/help/CODEHOP/CODEHOP_help.html","blocks",
23 "post","application/x-www-form-urlencoded");
24
25 option=new Array();
26 option[0]=new makeOption("primer3");
27 option[1]=new makeOption("codehop");
28
29 description=new Array();
30 description[0]=new makeDescription("primer3");
31 description[1]=new makeDescription("codehop");
32
33 /*********************************************************************
34 ******************** CUSTOMIZATION CODE *****************************
35 **********************************************************************/
36 /*Do not edit this tag*/
37 /**Section #2 code goes here**/
38
39 for(i=0;i<option.length;i++){
40 option[i].hideit();
41 }
42 writeprogrambanner();
43 showDescription();
44 }
45 </script>
46
47
48 </head>
49
50 <body bgcolor="white" topmargin="0" leftmargin="0" marginheight="0" marginwidth="0" alink="#cc0000" vlink="#cc0000" link="#cc0000" onload="init()">
51 <table border="0" cellpadding="0" cellspacing="0">
52 <tr>
53 <td bgcolor="#cc0000" width="10"><spacer type="block" width="10" height="32"></td>
54 <td width="528">
55 <table border="0" cellpadding="0" cellspacing="0" width="522">
56 <tr height="20">
57 <td width="20" height="20">&nbsp;</td>
58 <td height="20">&nbsp;</td>
59 </tr>
60 <tr>
61 <td width="20"></td>
62 <td><img height="21" width="268" src="images/pcrandrelated.png"></td>
63 </tr>
64 <tr height="20">
65 <td width="20" height="20"></td>
66 <td height="20"></td>
67 </tr>
68 <tr height="20">
69 <td width="20" height="20"></td>
70 <td class="body" height="20">
71 <table width="436" border="0" cellspacing="0" cellpadding="0" mm_noconvert="TRUE" height="190">
72 <tr>
73 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
74 <form name="programchoice">
75
76 <td class="size1" bgcolor="#cccccc" valign="middle" colspan="2"><img src="images/progselect.png" width="96" height="17"> <select name="program" size="1" onchange="programSelect()">
77 <option value="primer3" selected>Primer3
78 <option value="codehop">CODEHOP
79 <!--Do not edit this tag-->
80 <!--Section #3 code goes here-->
81 </select></td>
82 </form>
83
84 <td class="size1" bgcolor="#cccccc" colspan="2" valign="middle" align="right">
85 <div align="right">
86 <a href="javascript:check('submit')"><img src="images/submit.png" width="69" height="18" border="0" alt="Submit query"></a></div>
87 </td>
88 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
89 </tr>
90 <tr>
91 <td class="size1" bgcolor="#cccccc" colspan="4"><img src="images/query.png" width="47" height="17"></td>
92 </tr>
93 <tr>
94 <form name="query" onsubmit="javascript:check()">
95
96 <td class="size1" bgcolor="#e6e6e6" colspan="4" align="center" valign="middle"><textarea name="textfield" cols="50" rows="5"></textarea></td>
97 </form>
98 </tr>
99 <tr>
100 <td bgcolor="#cccccc" colspan="4"><spacer type="block" width="1" height="1"></td>
101 </tr>
102 <tr height="5">
103 <td bgcolor="white" height="5" width="86"><spacer type="block" width="1" height="5"></td>
104 <td bgcolor="white" height="5">&nbsp;</td>
105 <td bgcolor="white" align="right" height="5">&nbsp;</td>
106 <td bgcolor="white" align="right" height="5">&nbsp;</td>
107 </tr>
108 <tr>
109 <td bgcolor="white" width="86"><a href="javascript:optiontoggle()"><img name="optiontoggle" src="images/optionoff.png" width="65" height="20" border="0" alt="Click here to show/hide the option menu"></a></td>
110 <td bgcolor="white" align="left"><a href="javascript:check('customize')"><img border="0" height="10" width="56" src="images/customize.png"></a></td>
111 <td bgcolor="white"><a href="javascript:clearForm()"><img src="images/clear.png" width="35" height="15" border="0" alt="Clear this form"></a></td>
112 <td align="right"><a href="javascript:findhelp()"><img src="images/help.png" width="33" height="14" border="0" alt="Show help for the chosen program"></a></td>
113 </tr>
114 <tr height="1">
115 <td bgcolor="#cccccc" colspan="4" height="1"><spacer type="block" width="1" height="1"></td>
116 </tr>
117 </table>
118 <table border="0" cellpadding="0" cellspacing="0" width="435" height="197">
119 <tr>
120 <td class="body" valign="middle">
121 <ul type="square">
122 <li>Select the <b>program</b> of choice.
123 <li>Paste your query in the <b>query</b> box. Click <b>Submit button</b> to pass on the query with default options. Please note that <b>some programs might have some options/parameters that are required</b>. <b>Also note that SeWeR doesn't check whether the required option(s)/parameter(s) is supplied or not</b>. See program description for details.
124 <li>Click <b>Options button</b> to fill up options. The button is a toggle. Clicking it again will close the option.
125 <li>Click <b>Customize</b> to customize this search. Fill up all the options that you require, then click <b>Customize</b>. SeWeR will open another window with a customized page. Save that file on your computer.
126 <li>Click <b>Help</b> to check the help page of the selected program. SeWeR will open a new window to show the help page.
127 <li>Click <b>Submit</b> to pass on the query. SeWeR will open a new window for results.
128 </ul>
129 </td>
130 </tr>
131 </table>
132 </td>
133 </tr>
134 <tr height="1">
135 <td height="1" colspan="2" bgcolor="#cc0000"><spacer type="block" width="32" height="1"></td>
136 </tr>
137 <tr height="20">
138 <td width="20" height="20"></td>
139 <td height="20"><spacer type="block" width="32" height="20"></td>
140 </tr>
141 <tr height="1">
142 <td width="20" height="1"></td>
143 <td height="1" class="size1"><a href="home.htm">Home</a> | <a href="nucleicacid.htm">NucleicAcid</a> | <a href="protein.htm">Protein</a> | <a href="database.htm">Database</a> | <a href="pcr.htm">PCR</a> | <a href="align.htm">Alignment</a> | <a href="tools.htm">Tools</a> | <a href="bookmarklet.htm">Bookmarklets</a> | <a href="custom.htm">Customize</a>
144 <p><a href="copyright.htm"><font color="#666666">Copyright </font></a><font color="#666666">&copy; 2000, 2003, 2004 Malay Kumar Basu<br>
145 Send your comments/suggestions/bug-report to me:<br>
146 <a href="mailto:malay@bioinformatics.org">malay@bioinformatics.org</a><br>
147 <a href="copyright.htm">Disclaimer</a></font><br>
148 <br>
149 </td>
150 </tr>
151 </table>
152 </td>
153 <td width="1" bgcolor="#cc0000"><spacer type="block" width="1" height="32"></td>
154 </tr>
155 <tr height="2100">
156 <td><spacer type="block" width="1" height="2100"></td>
157 </tr>
158 </table>
159 <div id="programbanner"><p class="heading">Program Name</p>
160 </div>
161 <div id="result">
162 </div>
163 <div id="sewer"><img height="39" width="68" border="0" src="images/sewer_logo_small.png"></div>
164 <div id="primer3" class="optionlist">
165 <form name="primer3form" action="primer3_www_results.cgi" method="post" enctype="x-www-form-urlencoded">
166 <table width="572" border="0" cellpadding="5" cellspacing="0" height="2445" bgcolor="#e6e6e6">
167 <tr height="19">
168 <td colspan="4" class="size3" height="19"><font color="#cc0000"><b>primer3</b></font></td>
169 </tr>
170 <tr height="24">
171 <td colspan="4" class="size1" height="24"><b>Mispriming Library (repeat library)</b> <select name="PRIMER_MISPRIMING_LIBRARY" size="1">
172 <option selected value="">NONE
173 <option value="">HUMAN
174 <option value="">RODENT
175 </select></td>
176 </tr>
177 <tr height="46">
178 <td colspan="4" class="size1" height="46"><input type="checkbox" name="MUST_XLATE_PICK_LEFT" value="1" checked> <b>Pick left primer or use sequence</b><br>
179 <input type="text" size="30" name="PRIMER_LEFT_INPUT"></td>
180 </tr>
181 <tr height="37">
182 <td height="37" colspan="4" class="size1"><input type="checkbox" name="MUST_XLATE_PICK_HYB_PROBE"> <b>Pick hybridization probe or use oligo</b><br>
183 <input type="text" size="30" name="PRIMER_INTERNAL_OLIGO_INPUT"></td>
184 </tr>
185 <tr height="37">
186 <td height="37" colspan="4" class="size1"><input type="checkbox" name="MUST_XLATE_PICK_RIGHT" value="1" checked> <b>Pick right Primer or use sequence</b><br>
187 <input type="text" size="30" name="PRIMER_RIGHT_INPUT"></td>
188 </tr>
189 <tr height="37">
190 <td height="37" colspan="4" class="size1"><b>Sequence Id (a name to identify your sequence)</b><br>
191 <input type="text" name="PRIMER_SEQUENCE_ID" size="24"></td>
192 </tr>
193 <tr height="37">
194 <td height="37" colspan="4" class="size1"><b>Region the primers will flank</b> <input type="text" name="TARGET" size="24"><br>
195 Formats: [base number],[number of bases] e.g. 50,2 or mark the sequence with []</td>
196 </tr>
197 <tr height="37">
198 <td height="37" colspan="4" class="size1"><b>Excluded Region </b><input type="text" name="EXCLUDED_REGION" size="24"><br>
199 Formats:[base number],[number of bases] e.g. 401,7 68,3 or mark the sequence with &lt;&gt;</td>
200 </tr>
201 <tr height="37">
202 <td height="37" colspan="4" class="size1"><b>Product Size</b><br>
203 Min <input type="text" size="9" name="MUST_XLATE_PRODUCT_MIN_SIZE" value="100"> Opt <input type="text" size="9" name="PRIMER_PRODUCT_OPT_SIZE" value="200"> Max <input type="text" size="9" name="MUST_XLATE_PRODUCT_MAX_SIZE" value="1000"></td>
204 </tr>
205 <tr height="28">
206 <td height="28" colspan="3" class="size1"><b>Number of Return</b> <input type="text" size="4" name="PRIMER_NUM_RETURN" value="5"></td>
207 <td height="28" width="289" class="size1"><b>Max 3' Stability</b> <input type="text" size="4" name="PRIMER_MAX_END_STABILITY" value="9.0"></td>
208 </tr>
209 <tr height="40">
210 <td height="40" colspan="3" class="size1"><b>Max Mispriming</b> <input type="text" size="4" name="PRIMER_MAX_MISPRIMING" value="12.00"><br>
211 </td>
212 <td height="40" width="289" class="size1"><b>Pair Max Mispriming</b> <input type="text" size="4" name="PRIMER_PAIR_MAX_MISPRIMING" value="24.00"></td>
213 </tr>
214 <tr height="25">
215 <td height="25" colspan="4" class="size1"><font color="#cc0000"><b>General Primer Picking Conditions</b></font></td>
216 </tr>
217 <tr height="29">
218 <td height="29" colspan="4" class="size1"><b>Primer Size</b> Min <input type="text" size="4" name="PRIMER_MIN_SIZE" value="18"> Opt <input type="text" size="4" name="PRIMER_OPT_SIZE" value="20"> Max <input type="text" size="4" name="PRIMER_MAX_SIZE" value="27"></td>
219 </tr>
220 <tr height="40">
221 <td height="40" colspan="3" class="size1"><b>Primer Tm</b><br>
222 Min <input type="text" size="4" name="PRIMER_MIN_TM" value="57.0"> Opt <input type="text" size="4" name="PRIMER_OPT_TM" value="60.0"> Max <input type="text" size="4" name="PRIMER_MAX_TM" value="63.0"><br>
223 </td>
224 <td height="40" width="289" class="size1"><b>Max Tm Difference</b><input type="text" size="4" name="PRIMER_MAX_DIFF_TM" value="100.0"></td>
225 </tr>
226 <tr height="37">
227 <td height="37" colspan="3" class="size1"><b>Product Tm</b><br>
228 Min <input type="text" size="4" name="PRIMER_PRODUCT_MIN_TM"> Opt <input type="text" size="4" name="PRIMER_PRODUCT_OPT_TM"> Max <input type="text" size="4" name="PRIMER_PRODUCT_MAX_TM"></td>
229 <td height="37" width="289" class="size1"><b>Primer GC%</b><br>
230 Min <input type="text" size="4" name="PRIMER_MIN_GC" value="20.0"> Opt <input type="text" size="4" name="PRIMER_OPT_GC_PERCENT"> Max <input type="text" size="4" name="PRIMER_MAX_GC" value="80.0"></td>
231 </tr>
232 <tr height="31">
233 <td height="31" colspan="3" class="size1"><b>Max Self Complementarity</b><input type="text" size="4" name="PRIMER_SELF_ANY" value="8.00"></td>
234 <td height="31" width="289" class="size1"><b>Max 3' Self Complementarity<input type="text" size="4" name="PRIMER_SELF_END" value="3.00"> </b></td>
235 </tr>
236 <tr height="27">
237 <td height="27" colspan="3" class="size1"><b>Max #N's</b> <input type="text" size="4" name="PRIMER_NUM_NS_ACCEPTED" value="0"></td>
238 <td height="27" width="289" class="size1"><b>Max Poly-X</b> <input type="text" size="4" name="PRIMER_MAX_POLY_X" value="5"></td>
239 </tr>
240 <tr height="29">
241 <td height="29" colspan="3" class="size1"><b>Inside Target Penalty <input type="text" size="4" name="PRIMER_INSIDE_PENALTY"> </b></td>
242 <td height="29" width="289" class="size1"><b>Outside Target Penalty <input type="text" size="4" name="PRIMER_OUTSIDE_PENALTY" value="0"> </b></td>
243 </tr>
244 <tr height="23">
245 <td height="23" colspan="3" class="size1"><b>First Base Index <input type="text" size="4" name="PRIMER_FIRST_BASE_INDEX" value="1"> </b></td>
246 <td height="23" width="289" class="size1"><b>CG Clamp <input type="text" size="4" name="PRIMER_GC_CLAMP" value="0"> </b></td>
247 </tr>
248 <tr height="37">
249 <td height="37" colspan="3" class="size1"><b>Salt Concentration <input type="text" size="4" name="PRIMER_SALT_CONC" value="50.0"> </b></td>
250 <td height="37" width="289" class="size1"><b>Annealing Oligo Concentration <input type="text" size="4" name="PRIMER_DNA_CONC" value="50.0"> </b></td>
251 </tr>
252 <tr height="24">
253 <td height="24" colspan="3" class="size1"><b>Liberal Base <input type="checkbox" name="PRIMER_LIBERAL_BASE" value="1" checked> </b></td>
254 <td height="24" width="289" class="size1"><b>Show Debuging Info</b> <input type="checkbox" name="MUST_XLATE_PRINT_INPUT" value="1"></td>
255 </tr>
256 <tr height="37">
257 <td height="37" colspan="4" class="size1"><font color="#cc0000"><b>Other Per-Sequence Inputs </b></font></td>
258 </tr>
259 <tr height="37">
260 <td height="37" colspan="4" class="size1"><b>Included Region to pick primers <input type="text" name="INCLUDED_REGION" size="24"><br>
261 </b>Format: Starting Base number, length e.g. 20,400 or mark the sequence with{}</td>
262 </tr>
263 <tr height="37">
264 <td height="37" colspan="4" class="size1"><b>Start Codon Position <input type="text" name="PRIMER_START_CODON_POSITION" size="24"> </b></td>
265 </tr>
266 <tr height="37">
267 <td height="37" colspan="4" class="size1"><b>Sequence Quality<br>
268 <textarea rows="2" cols="40" name="PRIMER_SEQUENCE_QUALITY"> </textarea> </b></td>
269 </tr>
270 <tr height="37">
271 <td height="37" colspan="3" class="size1"><b>Min Sequence Quality <input type="text" size="4" name="PRIMER_MIN_QUALITY" value="0"> </b></td>
272 <td height="37" width="289" class="size1"><b>Min End Sequence Quality <input type="text" size="4" name="PRIMER_MIN_END_QUALITY" value="0"> </b></td>
273 </tr>
274 <tr height="36">
275 <td height="36" colspan="3" class="size1"><b>Sequence Quality Range Min <input type="text" size="4" name="PRIMER_QUALITY_RANGE_MIN" value="0"> </b></td>
276 <td height="36" width="289" class="size1"><b>Sequence Quality Range Max <input type="text" size="4" name="PRIMER_QUALITY_RANGE_MAX" value="100"> </b></td>
277 </tr>
278 <tr height="37">
279 <td height="37" colspan="4" class="size1"><font color="#cc0000"><b>Objective Function Penalty Weights for Primers</b></font></td>
280 </tr>
281 <tr height="209">
282 <td height="209" colspan="3" valign="top" class="size1">
283 <table border="0">
284 <tr>
285 <td class="size1"><b>Tm </b></td>
286 <td><b>Lt: </b></td>
287 <td class="size1"><b><input type="text" size="4" name="PRIMER_WT_TM_LT" value="1.0"> </b></td>
288 <td class="size1"><b>Gt: </b></td>
289 <td class="size1"><input type="text" size="4" name="PRIMER_WT_TM_GT" value="1.0"></td>
290 </tr>
291 <tr>
292 <td class="size1"><b>Size </b></td>
293 <td class="size1">Lt:</td>
294 <td class="size1"><b><input type="text" size="4" name="PRIMER_WT_SIZE_LT" value="1.0"> </b></td>
295 <td class="size1">Gt:<b> </b></td>
296 <td class="size1"><input type="text" size="4" name="PRIMER_WT_SIZE_GT" value="1.0"></td>
297 </tr>
298 <tr>
299 <td class="size1"><b>GC% </b></td>
300 <td class="size1">Lt:</td>
301 <td class="size1"><b><input type="text" size="4" name="PRIMER_WT_GC_PERCENT_LT" value="0.0"> </b></td>
302 <td class="size1">Gt:<b> </b></td>
303 <td class="size1"><input type="text" size="4" name="PRIMER_WT_GC_PERCENT_GT" value="0.0"></td>
304 </tr>
305 </table>
306 </td>
307 <td height="209" width="289" class="size1" valign="top">
308 <table border="0" width="216">
309 <tr>
310 <td width="172" class="size1"><b>Self Complementarity </b></td>
311 <td width="23" class="size1"><input type="text" size="4" name="PRIMER_WT_COMPL_ANY" value="0.0"></td>
312 </tr>
313 <tr>
314 <td width="172" class="size1"><b>3' Self Complementarity </b></td>
315 <td width="23" class="size1"><input type="text" size="4" name="PRIMER_WT_COMPL_END" value="0.0"></td>
316 </tr>
317 <tr>
318 <td width="172" class="size1"><b>#N's </b></td>
319 <td width="23" class="size1"><input type="text" size="4" name="PRIMER_WT_NUM_NS" value="0.0"></td>
320 </tr>
321 <tr>
322 <td width="172" class="size1"><b>Mispriming </b></td>
323 <td width="23"><input type="text" size="4" name="PRIMER_WT_REP_SIM" value="0.0"></td>
324 </tr>
325 <tr>
326 <td width="172" class="size1"><b>Sequence Quality </b></td>
327 <td width="23" class="size1"><input type="text" size="4" name="PRIMER_WT_SEQ_QUAL" value="0.0"></td>
328 </tr>
329 <tr>
330 <td width="172" class="size1"><b>End Sequence Quality </b></td>
331 <td width="23" class="size1"><input type="text" size="4" name="PRIMER_WT_END_QUAL" value="0.0"></td>
332 </tr>
333 <tr>
334 <td width="172" class="size1"><b>Position Penalty </b></td>
335 <td width="23" class="size1"><input type="text" size="4" name="PRIMER_WT_POS_PENALTY" value="0.0"></td>
336 </tr>
337 <tr>
338 <td width="172" class="size1"><b>End Stability </b></td>
339 <td width="23" class="size1"><input type="text" size="4" name="PRIMER_WT_END_STABILITY" value="0.0"></td>
340 </tr>
341 </table>
342 </td>
343 </tr>
344 <tr height="32">
345 <td height="32" colspan="4" class="size1"><font color="#cc0000"><b>Objective Function Penalty Weights for PrimerPairs</b></font></td>
346 </tr>
347 <tr height="41">
348 <td height="41" colspan="3" valign="top" class="size1">
349 <table border="0" width="282">
350 <tr>
351 <td class="size1"><b>Product Size </b></td>
352 <td class="size1">Lt:</td>
353 <td class="size1"><b><input type="text" size="4" name="PRIMER_PAIR_WT_PRODUCT_SIZE_LT" value="0.05"> </b></td>
354 <td class="size1">Gt:</td>
355 <td class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_PRODUCT_SIZE_GT" value="0.05"></td>
356 </tr>
357 <tr>
358 <td class="size1"><b>Product Tm </b></td>
359 <td class="size1">Lt:</td>
360 <td class="size1"><b><input type="text" size="4" name="PRIMER_PAIR_WT_PRODUCT_TM_LT" value="0.0"> </b></td>
361 <td class="size1">Gt:</td>
362 <td class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_PRODUCT_TM_GT" value="0.0"></td>
363 </tr>
364 </table>
365 </td>
366 <td height="41" width="289" class="size1" valign="top">
367 <table border="0" width="277">
368 <tr>
369 <td width="208" class="size1"><b>Tm Difference </b></td>
370 <td width="59" class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_DIFF_TM" value="0.0"></td>
371 </tr>
372 <tr>
373 <td width="208" class="size1"><b>Any Complementarity </b></td>
374 <td width="59" class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_COMPL_ANY" value="0.0"></td>
375 </tr>
376 <tr>
377 <td width="208" class="size1"><b>3' Complementarity </b></td>
378 <td width="59" class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_COMPL_END" value="0.0"></td>
379 </tr>
380 <tr>
381 <td width="208" class="size1"><b>Pair Mispriming </b></td>
382 <td width="59" class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_REP_SIM" value="0.0"></td>
383 </tr>
384 <tr>
385 <td width="208" class="size1"><b>Primer Penalty Weight </b></td>
386 <td width="59" class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_PR_PENALTY" value="1.0"></td>
387 </tr>
388 <tr>
389 <td width="208" class="size1"><b>Hyb Oligo Penalty Weight </b></td>
390 <td width="59" class="size1"><input type="text" size="4" name="PRIMER_PAIR_WT_IO_PENALTY" value="0.0"></td>
391 </tr>
392 </table>
393 </td>
394 </tr>
395 <tr height="21">
396 <td height="21" colspan="4" valign="top" class="size1"><font color="#cc0000"><b>Hyb Oligo (Internal Oligo) Per-Sequence Inputs</b></font></td>
397 </tr>
398 <tr height="16">
399 <td height="16" colspan="4" valign="top" class="size1"><b>Hyb Oligo Excluded Region </b><input type="text" name="PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION" size="24"></td>
400 </tr>
401 <tr height="19">
402 <td height="19" colspan="4" valign="top"><font color="#cc0000" class="size1"><b>Hyb Oligo (Internal Oligo) General Conditions</b></font></td>
403 </tr>
404 <tr height="41">
405 <td height="41" colspan="4" valign="top" class="size1">
406 <table border="0">
407 <tr>
408 <td class="size1"><b>Hyb Oligo Size: </b></td>
409 <td class="size1">Min <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MIN_SIZE" value="18"></td>
410 <td class="size1">Opt <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_OPT_SIZE" value="20"></td>
411 <td class="size1">Max <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MAX_SIZE" value="27"></td>
412 </tr>
413 <tr>
414 <td class="size1"><b>Hyb Oligo Tm: </b></td>
415 <td class="size1">Min <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MIN_TM" value="57.0"></td>
416 <td class="size1">Opt <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_OPT_TM" value="60.0"></td>
417 <td class="size1">Max <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MAX_TM" value="63.0"></td>
418 </tr>
419 <tr>
420 <td class="size1"><b>Hyb Oligo GC% </b></td>
421 <td class="size1">Min: <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MIN_GC" value="20.0"></td>
422 <td class="size1">Opt: <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT"></td>
423 <td class="size1">Max: <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MAX_GC" value="80.0"></td>
424 </tr>
425 </table>
426 </td>
427 </tr>
428 <tr height="26">
429 <td height="26" colspan="4" valign="top" class="size1"><b>Hyb Oligo Self Complementarity <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_SELF_ANY" value="12.00"> </b></td>
430 </tr>
431 <tr height="27">
432 <td height="27" colspan="4" valign="top" class="size1"><b>Hyb Oligo Max 3' Self Complementarity: <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_SELF_END" value="12.00"> </b></td>
433 </tr>
434 <tr height="28">
435 <td height="28" colspan="4" valign="top" class="size1"><b>Hyb Oligo DNA Concentration <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_DNA_CONC" value="50.0"> </b></td>
436 </tr>
437 <tr height="27">
438 <td height="27" colspan="4" valign="top" class="size1"><b>Hyb Oligo Salt Concentration: <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_SALT_CONC" value="50.0"> </b></td>
439 </tr>
440 <tr height="25">
441 <td height="25" colspan="4" valign="top" class="size1"><b>Hyb Oligo Min Sequence Quality <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MIN_QUALITY" value="0"> </b></td>
442 </tr>
443 <tr height="21">
444 <td height="21" colspan="4" valign="top" class="size1"><b>Hyb Oligo Mishyb Library <select name="PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY" size="1">
445 <option selected value="">NONE
446 </select> </b></td>
447 </tr>
448 <tr height="24">
449 <td height="24" colspan="4" valign="top" class="size1"><b>Hyb Oligo Max Mishyb: <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MAX_MISHYB" value="12.00"> </b></td>
450 </tr>
451 <tr height="42">
452 <td height="42" colspan="4" valign="top" class="size1"><b>Hyb Oligo Max Poly-X: <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_MAX_POLY_X" value="5"> Max #Ns <input type="text" size="4" name="PRIMER_INTERNAL_OLIGO_NUM_NS" value="0"> </b></td>
453 </tr>
454 <tr height="22">
455 <td height="22" colspan="4" valign="top" class="size1"><font color="#cc0000"><b>Objective Function Penalty Weights for Hyb Oligos (Internal Oligos) </b></font></td>
456 </tr>
457 <tr height="22">
458 <td height="22" colspan="3" valign="top" class="size1">
459 <table border="0">
460 <tr>
461 <td colspan="5" class="size1"><b>Hyb Oligo Tm<br>
462 </b>Lt: <input type="text" size="4" name="PRIMER_IO_WT_TM_LT" value="1.0"> Gt: <b><input type="text" size="4" name="PRIMER_IO_WT_TM_GT" value="1.0"> </b></td>
463 </tr>
464 <tr>
465 <td colspan="5" class="size1"><b>Hyb Oligo Size<br>
466 </b>Lt: <input type="text" size="4" name="PRIMER_IO_WT_SIZE_LT" value="1.0"> Gt: <input type="text" size="4" name="PRIMER_IO_WT_SIZE_GT" value="1.0"></td>
467 </tr>
468 <tr>
469 <td colspan="5" class="size1"><b>Hyb Oligo GC%<br>
470 </b>Lt: <input type="text" size="4" name="PRIMER_IO_WT_GC_PERCENT_LT" value="0.0"> Gt: <input type="text" size="4" name="PRIMER_IO_WT_GC_PERCENT_GT" value="0.0"></td>
471 </tr>
472 </table>
473 </td>
474 <td height="22" width="289" valign="top" class="size1">
475 <table border="0" width="263">
476 <tr>
477 <td class="size1" width="186"><b>Hyb Oligo Self Complementarity </b></td>
478 <td class="size1" width="68"><b><input type="text" size="4" name="PRIMER_IO_WT_COMPL_ANY" value="0.0"> </b></td>
479 </tr>
480 <tr>
481 <td width="186" class="size1"><b>Hyb Oligo #N's </b></td>
482 <td width="68" class="size1"><b><input type="text" size="4" name="PRIMER_IO_WT_NUM_NS" value="0.0"> </b></td>
483 </tr>
484 <tr>
485 <td width="186" class="size1"><b>Hyb Oligo Mishybing </b></td>
486 <td width="68" class="size1"><b><input type="text" size="4" name="PRIMER_IO_WT_REP_SIM" value="0.0"> </b></td>
487 </tr>
488 <tr>
489 <td width="186" class="size1"><b>Hyb Oligo Sequence Quality </b></td>
490 <td width="68" class="size1"><b><input type="text" size="4" name="PRIMER_IO_WT_SEQ_QUAL" value="0.0"> </b></td>
491 </tr>
492 </table>
493 </td>
494 </tr>
495 <tr height="22">
496 <td height="22" colspan="4" valign="top" class="size1"><input type="hidden" name="Pick Primers" value="Pick Primers"></td>
497 </tr>
498 </table>
499 </form>
500 </div>
501
502
503 <div id="codehop" class="optionlist">
504 <form name="codehopform" action="/blocks-bin/codehop.pl" method="post">
505 <table width="600" border="0" cellspacing="0" cellpadding="5" bgcolor="#e6e6e6">
506 <tr>
507 <td class="size3" colspan="2"><font color="#cc0000"><b>codehop</b></font></td>
508 </tr>
509 <tr>
510 <td class="size1" colspan="2"><b>Core (degenerate 3' region)</b></td>
511 </tr>
512 <tr>
513 <td class="size1" width="287">Degeneracy <input name="core_degen" size="5" value="128" type="text"></td>
514 <td class="size1" width="307">Strictness <input name="core_strict" size="5" value="0.0" type="text"></td>
515 </tr>
516 <tr>
517 <td class="size1" colspan="2"><b>Clamp (non-degenerate 5' region)</b></td>
518 </tr>
519 <tr>
520 <td class="size1" width="287">Temperature <input name="clamp_temp" size="5" value="60.0" type="text"></td>
521 <td class="size1" width="307">Poly-nuc <input name="polyx" size="5" value="5" type="text"></td>
522 </tr>
523 <tr>
524 <td class="size1" colspan="2"><b>Primer concentration [in nM]</b> <input name="TEMP" size="5" value="50" type="text"></td>
525 </tr>
526 <tr>
527 <td class="size1" colspan="2"><b>Codon usage table</b> <select name="codonuse" size="1">
528 <option value="">------gbbct------
529 <option value="agro.codon.use">Agrobacterium tumefaciens
530 <option value="bacsub.codon.use">Bacillus subtilis
531 <option value="bact.codon.use">Bacillus thuringiensis
532 <option value="bartb.codon.use">Bartonella bacilliformis
533 <option value="barth.codon.use">Bartonella henselae
534 <option value="chlam.codon.use">Chlamydia trachomatis
535 <option value="ehrl.codon.use">Ehrlichia chaffeensis
536 <option value="ecoli.codon.use">Escherichia coli
537 <option value="lacto.codon.use">Lactobacillus casei
538 <option value="pseudo.codon.use">Pseudomonas syringae pv. glycinea
539 <option value="ralston.codon.use">Ralstonia eutropha
540 <option value="rhodo.codon.use">Rhodobacter sphaeroides
541 <option value="staph.codon.use">Staphylococcus aureus
542 <option value="strep.codon.use">Streptomyces coelicolor
543 <option value="">------gbinv------
544 <option value="ancyl.codon.use">Ancylostoma canium
545 <option value="ascaris.codon.use">Ascaris suum
546 <option value="bombyx.codon.use">Bombyx mori
547 <option value="brugia.codon.use">Brugia malayi
548 <option value="worm.codon.use">Caenorhabditis elegans
549 <option value="fly.codon.use">Drosophila melanogaster
550 <option value="giardia.codon.use">Giardia intestinalis
551 <option value="haem.codon.use">Haemonchus contortus
552 <option value="hirudo.codon.use">Hirudo medicinalis
553 <option value="hydra.codon.use">Hydra vulgaris
554 <option value="leishm.codon.use">Leishmania major
555 <option value="leish.codon.use">Leishmania tarentolae
556 <option value="lymn.codon.use">Lymnaea stagnalis
557 <option value="musca.codon.use">Musca domestica
558 <option value="onch.codon.use">Onchocerca volvulus
559 <option value="placo.codon.use">Placopecten magellanicus
560 <option value="plasmo.codon.use">Plasmodium falciparum
561 <option value="schis.codon.use">Schistosoma mansoni
562 <option value="strongy.codon.use">Strongylocentrotus purpuratus
563 <option value="tetra.codon.use">Tetrahymena thermophila
564 <option value="trich.codon.use">Trichinella spiralis
565 <option value="tryp.codon.use">Trypanosoma brucei
566 <option value="">------gbmam------
567 <option value="cow.codon.use">Bos taurus
568 <option value="rabbit.codon.use">Oryctolagus cuniculus
569 <option value="sheep.codon.use">Ovis aries
570 <option value="pig.codon.use">Sus scrofa
571 <option value="">------gbpln------
572 <option value="arab.codon.use">Arabadopsis thaliana
573 <option value="napus.codon.use">Brassica napus
574 <option value="broc.codon.use">Brassica oleracea
575 <option value="chlamy.codon.use">Chlamydomonas reinhardtii
576 <option value="barley.codon.use">Hordeum vulgare
577 <option value="tomato.codon.use">Lycopersicon esculentum
578 <option value="apple.codon.use">Malus domestica
579 <option value="iceplant.codon.use">Mesembryanthemum crystallinum
580 <option value="neur.codon.use">Neurospora crassa
581 <option value="tobacco.codon.use">Nicotiana tabacum
582 <option value="rice.codon.use">Oryza sativa
583 <option value="moss.codon.use">Physcomitrella patens
584 <option value="porph.codon.use">Porphyra pulchra
585 <option value="peach.codon.use">Prunus persica
586 <option value="yeast.codon.use">Saccharomyces cerevisiae
587 <option value="pombe.codon.use">Schizosaccharomyces pombe
588 <option value="potato.codon.use">Solanum tuberosum
589 <option value="ustilago.codon.use">Ustilago maydis
590 <option value="zea.codon.use">Zea mays
591 <option value="">------gbpri------
592 <option selected value="human.codon.use">Homo sapiens
593 <option value="">------gbrod------
594 <option value="cavia.codon.use">Cavia porcellus
595 <option value="mouse.codon.use">Mus musculus
596 <option value="rat.codon.use">Rattus norvegicus
597 <option value="">------gbvrl------
598 <option value="civ.codon.use">Chilo iridescent virus
599 <option value="">------gbvrt------
600 <option value="amby.codon.use">Ambystoma mexicanum
601 <option value="anas.codon.use">Anas platyrhynchos
602 <option value="duck.codon.use">Cairina moschata
603 <option value="zebra.codon.use">Danio rerio
604 <option value="fugu.codon.use">Fugu rubripes
605 <option value="chicken.codon.use">Gallus gallus
606 <option value="frog.codon.use">Xenopus laevis
607 <option value="">------other------
608 <option value="eukaryotic.codon.use">Eukaryotic average
609 <option value="default.codon.use">Equal
610 </select></td>
611 </tr>
612 <tr>
613 <td class="size1" colspan="2"><b>Show the</b> <input name="outoligo2" size="3" value="3" type="text"> <b>least degenerate, or show all overlapping primers</b> <input name="verbose2" type="checkbox" value="TRUE"></td>
614 </tr>
615 <tr>
616 <td class="size1" colspan="2"><b>Use core strictness for the 3' base</b> <input name="begin" type="checkbox" value="TRUE"></td>
617 </tr>
618 <tr>
619 <td class="size1" colspan="2"><b>Force the core/clamp boundary to be a codon boundary</b> <input name="rose" type="checkbox" value="TRUE"></td>
620 </tr>
621 <tr>
622 <td class="size1" colspan="2"><b>Use the most common codons in the clamp</b> <input name="most" type="checkbox" value="TRUE"></td>
623 </tr>
624 </table>
625 </form>
626 </div>
627 <div id="primer3description" class="description">
628 <table border="0" cellpadding="0" cellspacing="0" width="204">
629 <tr>
630 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>Primer3</b></td>
631 <td align="right"><a href="http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
632 </tr>
633 <tr height="1">
634 <td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td>
635 </tr>
636 <tr>
637 <td colspan="2" class="size1">Create PCR primers and Hybridization oligos from a DNA sequence. Input, DNA sequence. Required option-field, none.<br>
638 </td>
639 </tr>
640 </table>
641 </div>
642 <div id="codehopdescription" class="description">
643 <table border="0" cellpadding="0" cellspacing="0" width="204">
644 <tr>
645 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>CODEHOP</b></td>
646 <td align="right"><a href="http://bioinformatics.weizmann.ac.il/blocks/codehop.html" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
647 </tr>
648 <tr height="1">
649 <td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td>
650 </tr>
651 <tr>
652 <td colspan="2" class="size1">Pick primers from multiple alingnment of protein sequences. Input type, BLOCKS. Required option-field, none.</td>
653 </tr>
654 </table>
655 </div>
656
657 <!--Do not edit this tag-->
658 <!--Section #4 and #5 goes here-->
659
660 </body>
661
662 </html>