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Revision: 1.2
Committed: Sat Aug 28 06:04:38 2004 UTC (15 years, 7 months ago) by malay
Branch: MAIN
CVS Tags: HEAD
Changes since 1.1: +4 -4 lines
Log Message:
Fixed nucleicacid.htm

Line File contents
1 <html>
2 <head>
3 <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
4 <meta name="author" content="Dr Malay K Basu">
5 <!--Do not edit this tag-->
6 <!--Section #1 code goes here-->
7 <!--included_programs="entrez,protparam,psipred,scanprosite"-->
8 <!--Section #1 code goes here-->
9 <title>SeWeR: Protein Sequence Analysis</title>
10
11 <script language="JavaScript" src="scripts/browser.js"></script>
12 <script language="JavaScript1.2" src="scripts/sewer.js"></script>
13
14 <script language="JavaScript1.2">
15 function init(){
16
17 if(isNS6){
18 document.all=document.getElementsByTagName("*");
19 }
20 program=new Array();
21 program[0]=new ProgramConstructor("entrez","http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=Protein","http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?SUBMIT=y","http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html#Using Limits","term","post","application/x-www-form-urlencoded");
22 program[1]=new ProgramConstructor("protparam","http://us.expasy.org/tools/protparam.html","http://us.expasy.org/cgi-bin/protparam","http://us.expasy.org/tools/protparam.html","sequence","post","application/x-www-form-urlencoded");
23
24 program[2]=new ProgramConstructor("psipred","http://bioinf.cs.ucl.ac.uk/psipred/","http://bioinf.cs.ucl.ac.uk/cgi-bin/psipred/psipred.cgi","http://bioinf.cs.ucl.ac.uk/psipred/psipred_help.html","Sequence","post","x-www-form-urlencoded");
25
26
27 program[3]=new ProgramConstructor("scanprosite","http://us.expasy.org/tools/scanprosite/","http://us.expasy.org/cgi-bin/scanprosite","http://us.expasy.org/tools/scanprosite/","seq","post","application/x-www-form-urlencoded");
28
29
30 option=new Array();
31 option[0]=new makeOption("entrez");
32 option[1]=new makeOption("protparam")
33 option[2]=new makeOption("psipred")
34 option[3]=new makeOption("scanprosite")
35
36 description=new Array();
37 description[0]=new makeDescription("entrez");
38 description[1]=new makeDescription("protparam");
39 description[2]=new makeDescription("psipred");
40 description[3]=new makeDescription("scanprosite");
41
42 /*********************************************************************
43 ******************** CUSTOMIZATION CODE *****************************
44 **********************************************************************/
45 /*Do not edit this tag*/
46 /**Section #2 code goes here**/
47
48 for(i=0;i<option.length;i++){
49 option[i].hideit();
50 }
51 writeprogrambanner();
52 showDescription();
53 }
54 </script>
55
56
57 </head>
58
59 <body bgcolor="white" topmargin="0" leftmargin="0" marginheight="0" marginwidth="0" alink="#cc0000" vlink="#cc0000" link="#cc0000" onload="init()">
60 <table border="0" cellpadding="0" cellspacing="0">
61 <tr>
62 <td bgcolor="#cc0000" width="10"><spacer type="block" width="10" height="32"></td>
63 <td width="528">
64 <table border="0" cellpadding="0" cellspacing="0" width="522">
65 <tr height="20">
66 <td width="20" height="20">&nbsp;</td>
67 <td height="20">&nbsp;</td>
68 </tr>
69 <tr>
70 <td width="20"></td>
71 <td><img height="24" width="308" src="images/proteinhead.png"></td>
72 </tr>
73 <tr height="20">
74 <td width="20" height="20"></td>
75 <td height="20"></td>
76 </tr>
77 <tr height="20">
78 <td width="20" height="20"></td>
79 <td class="body" height="20">
80 <table width="436" border="0" cellspacing="0" cellpadding="0" mm_noconvert="TRUE" height="190">
81 <tr>
82 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
83 <form name="programchoice">
84
85 <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()">
86 <option value="entrez" selected>Entrez
87 <option value="protparam">Protparam
88 <option value="psipred">PSIPRED
89 <option value="scanprosite">ScanProsite
90 <!--Do not edit this tag-->
91 <!--Section #3 code goes here-->
92 </select></td>
93 </form>
94
95 <td class="size1" bgcolor="#cccccc" colspan="2" valign="middle" align="right">
96 <div align="right">
97 <a href="javascript:check('submit')"><img src="images/submit.png" width="69" height="18" border="0" alt="Submit query"></a></div>
98 </td>
99 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
100 </tr>
101 <tr>
102 <td class="size1" bgcolor="#cccccc" colspan="4"><img src="images/query.png" width="47" height="17"></td>
103 </tr>
104 <tr>
105 <form name="query" onsubmit="javascript:check()">
106
107 <td class="size1" bgcolor="#e6e6e6" colspan="4" align="center" valign="middle"><textarea name="textfield" cols="50" rows="5"></textarea></td>
108 </form>
109 </tr>
110 <tr>
111 <td bgcolor="#cccccc" colspan="4"><spacer type="block" width="1" height="1"></td>
112 </tr>
113 <tr height="5">
114 <td bgcolor="white" height="5" width="86"><spacer type="block" width="1" height="5"></td>
115 <td bgcolor="white" height="5">&nbsp;</td>
116 <td bgcolor="white" align="right" height="5">&nbsp;</td>
117 <td bgcolor="white" align="right" height="5">&nbsp;</td>
118 </tr>
119 <tr>
120 <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>
121 <td bgcolor="white" align="left"><a href="javascript:check('customize')"><img border="0" height="10" width="56" src="images/customize.png"></a></td>
122 <td bgcolor="white"><a href="javascript:clearForm()"><img src="images/clear.png" width="35" height="15" border="0" alt="Clear this form"></a></td>
123 <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>
124 </tr>
125 <tr height="1">
126 <td bgcolor="#cccccc" colspan="4" height="1"><spacer type="block" width="1" height="1"></td>
127 </tr>
128 </table>
129 <table border="0" cellpadding="0" cellspacing="0" width="435" height="197">
130 <tr>
131 <td class="body" valign="middle">
132 <ul type="square">
133 <li>Select the <b>program</b> of choice.
134 <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.
135 <li>Click <b>Options button</b> to fill up options. The button is a toggle. Clicking it again will close the option.
136 <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.
137 <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.
138 <li>Click <b>Submit</b> to pass on the query. SeWeR will open a new window for results.
139 </ul>
140 </td>
141 </tr>
142 </table>
143 </td>
144 </tr>
145 <tr height="1">
146 <td height="1" colspan="2" bgcolor="#cc0000"><spacer type="block" width="32" height="1"></td>
147 </tr>
148 <tr height="20">
149 <td width="20" height="20"></td>
150 <td height="20"><spacer type="block" width="32" height="20"></td>
151 </tr>
152 <tr height="1">
153 <td width="20" height="1"></td>
154 <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>
155 <p><a href="copyright.htm"><font color="#666666">Copyright </font></a><font color="#666666">&copy; 2000, 2003, 2004 Malay Kumar Basu<br>
156 Send your comments/suggestions/bug-report to me:<br>
157 <a href="mailto:malay@bioinformatics.org">malay@bioinformatics.org</a><br>
158 <a href="copyright.htm">Disclaimer</a></font><br>
159 <br>
160 </td>
161 </tr>
162 </table>
163 </td>
164 <td width="1" bgcolor="#cc0000"><spacer type="block" width="1" height="32"></td>
165 </tr>
166
167 </table>
168
169 <div id="programbanner"><p class="heading">Program Name</p></div>
170 <div id="result"></div>
171 <div id="sewer"><img height="39" width="68" border="0" src="images/sewer_logo_small.png"></div>
172 <div id="entrezoption" class="optionlist">
173 <form name="entrezform">
174 <table width="600" border="0" cellspacing="0" cellpadding="10" bgcolor="#e6e6e6">
175 <tr>
176 <td colspan="3" class="size3"><font color="#cc0000"><b>entrez protein search</b></font></td>
177 </tr>
178 <tr>
179 <td class="size1" width="172"><b>Search</b> <select name="defaultField" size="1">
180 <option value="Accession">Accession
181 <option selected value="All Fields">All Fields
182 <option value="Author Name">Author Name
183 <option value="EC/RN Number">EC/RN Number
184 <option value="Filter">Filter
185 <option value="Gene Name">Gene Name
186 <option value="Issue">Issue
187 <option value="Journal Name">Journal Name
188 <option value="Keyword">Keyword
189 <option value="Modification Date">Modification Date
190 <option value="Organism">Organism
191 <option value="Page Number">Page Number
192 <option value="Primary Accession">Primary Accession
193 <option value="Properties">Properties
194 <option value="Protein Name">Protein Name
195 <option value="Publication Date">Publication Date
196 <option value="SeqID String">SeqID String
197 <option value="Sequence Length">Sequence Length
198 <option value="Substance Name">Substance Name
199 <option value="Text Word">Text Word
200 <option value="Title Word">Title Word
201 <option value="Uid">Uid
202 <option value="Volume">Volume
203 </select></td>
204 <td class="size1" width="179"><input name="pmfilter_Exclude" type="checkbox" value="exclude patents"> <b>exclude patents&nbsp; </b></td>
205 <td class="size1" width="189">&nbsp;</td>
206 </tr>
207 <tr>
208 <td class="size1" width="172"><select name="pmfilter_GeneLoc" size="1">
209 <option value="">Gene Location
210 <option value="">Genomic DNA/RNA
211 <option value="">Mitochondrion
212 <option value="">Chloroplast
213 </select></td>
214 <td class="size1" width="179"><select name="pmfilter_SegSeq" size="1">
215 <option value="">Segmented Sequences
216 <option value="">Show only master of set
217 <option value="">Show only parts of set
218 </select></td>
219 <td class="size1" width="189"><select name="pmfilter_OnlyFrom" size="1">
220 <option value="">Only from
221 <option value="">RefSeq
222 <option value="">GenBank
223 <option value="">EMBL
224 <option value="">DDBJ
225 <option value="">PDB
226 <option value="">SWISS-PROT
227 <option value="">PIR
228 <option value="">PRF
229 </select></td>
230 </tr>
231 <tr>
232 <td class="size1" width="172"><select name="pmfilter_MDatLimit" size="1">
233 <option value="">Modification Date
234 <option value="">30 Days
235 <option value="">60 Days
236 <option value="">90 Days
237 <option value="">180 Days
238 <option value="">1 Year
239 <option value="">2 Years
240 <option value="">5 Years
241 <option value="">10 Years
242 </select></td>
243 <td class="size1" colspan="2"><select name="pmfilter_DateRange_Field" size="1">
244 <option value="">Modification Date
245 <option value="">Publication Date
246 </select> From <input maxlength="4" name="pmfilter_DateRange_MinYear" size="4" type="text"> <input maxlength="2" name="pmfilter_DateRange_MinMonth" size="2" type="text"> <input maxlength="2" name="pmfilter_DateRange_MinDay" size="2" type="text"> To <input maxlength="4" name="pmfilter_DateRange_MaxYear" size="4" type="text"> <input maxlength="2" name="pmfilter_DateRange_MaxMonth" size="2" type="text"> <input maxlength="2" name="pmfilter_DateRange_MaxDay" size="2" type="text"><br>
247 Use the format YYYY/MM/DD; month and day are optional.</td>
248 </tr>
249 </table>
250 <input name="db" type="hidden" value="Protein"> <input name="orig_db" type="hidden" value="Protein"> <input name="cmd" type="hidden" value="search"> <input name="cmd_current" type="hidden" value="Limits">
251 </form>
252 </div>
253 <!--Protparam-->
254 <div id="protparamoption" class="optionlist">
255 <form name="protparamform">
256 <table width="600" border="0" bgcolor="#e6e6e6" cellpadding="5" cellspacing="5">
257 <tr><td class="size1"><p class="size2"><font color="#cc0000"><b>protparam</b></font></p>
258
259 <p><b>Enter a Swiss-Prot/TrEMBL accession number (AC) (for example P05130) or a sequence identifier (ID) (for example KPC1_DROME)
260 </b>
261 <input type="text" size="15" name="prot_id" value=""></td></tr></table>
262 </form></div>
263 <!--Psipred-->
264 <div id="psipredoption" class="optionlist">
265 <form name="psipredform">
266 <table width="600" border="0" bgcolor="#e6e6e6" cellpadding="5" cellspacing="5">
267 <tr><td class="size1"><p class="size2"><font color="#cc0000"><b>psipred</b></font></p><hr size="1" noshade>
268 <p><span class="size2" style="color:#cc0000;font-weight:bold">Prediction method</span><p>
269 <input type="radio" name="Program" value="psipred" checked>
270 <b>Predict Secondary Structure (PSIPRED v2.3)</b><p>
271 <input type="radio" name="Program" value="memsat">
272 <b>Predict Transmembrane Topology (MEMSAT)</b><p>
273 <input type="radio" name="Program" value="genthreader">
274 <b>Fold Recognition(GenTHREADER - quick)</b><p>
275 <input type="radio" name="Program" value="mgenthreader">
276 <b>Fold Recognition (mGenTHREADER - with profiles and predicted secondary structure)
277 </b><p><hr size="1" noshade>
278 <p><span class="size2" style="color:#cc0000;font-weight:bold">Output options</span><p>
279 <input type="radio" name="Output" value="opnone" checked>
280 <b>Don't return PSI-BLAST output (default)</b><p>
281 <input type="radio" name="Output" value="ophits">
282 <b>Return PSI-BLAST hits only</b><p>
283 <input type="radio" name="Output" value="opaln">
284 <b>Return PSI-BLAST hits and alignments</b>
285 <p><hr size="1" noshade>
286 <p><b>E-mail address (required) </b>
287 <input type="text" size="15" name="Email" value="">
288 <p><b>Password (only required for commercial e-mail addresses)</b>
289 <input type="text" size="15" name="Passwd" value="">
290 <p><b>Short name for sequence</b>
291 <input type="text" size="15" name="Subject" value=""></td></tr></table>
292 </form></div>
293 <!--scanprosite-->
294 <div id="scanprositeoption" class="optionlist">
295 <form name="scanprositeform">
296 <table width="600" border="0" bgcolor="#e6e6e6" cellpadding="5" cellspacing="5">
297 <tr><td class="size1"><p class="size2"><font color="#cc0000"><b>scanprosite</b></font></p>
298 <p>
299 <input type="checkbox" name="type" value="p" checked>
300 <b>Scan patterns</b><p>
301 <input type="checkbox" name="type" value="m" checked>
302 <b>Scan profiles</b><p>
303 <input type="checkbox" name="type" value="r" checked>
304 <b>Scan rules</b><p>
305 <input type="checkbox" name="skip" value="on">
306 <b>Exclude patterns with a high probability of occurrence</b><p>
307 </td></tr></table>
308 </form></div>
309
310 <div id="entrezdescription" class="description">
311 <table border="0" cellpadding="0" cellspacing="0" width="204">
312 <tr>
313 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>Entrez</b></td>
314 <td align="right"><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=Protein" target="_blank"><img height="12" width="32" border="0" src="images/more_grey.png"></a></td>
315 </tr>
316 <tr height="1">
317 <td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td>
318 </tr>
319 <tr>
320 <td colspan="2" class="size1">Search for a protein sequence using Enterz at NCBI server. Input type-key-words. Required option-none.<br>
321 </td>
322 </tr>
323 </table>
324 </div>
325 <div id="protparamdescription" class="description">
326 <table border="0" cellpadding="0" cellspacing="0" width="204">
327 <tr>
328 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>ProtParam</b></td>
329 <td align="right"><a href="http://us.expasy.org/tools/protparam.html" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
330 </tr>
331 <tr><td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td></tr><tr><td colspan="2" class="size1">Calculate different physico-chemical parameters of a protein sequence. Input type-protein sequence. Required option-none</td></tr></table>
332 </div>
333 <div id="psipreddescription" class="description">
334 <table border="0" cellpadding="0" cellspacing="0" width="204">
335 <tr>
336 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>PSIPRED</b></td>
337 <td align="right"><a href="http://bioinf.cs.ucl.ac.uk/psipred/" target="_blank"><img height="12" width="32" border="0" src="images/more_grey.png"></a></td>
338 </tr>
339 <tr height="1">
340 <td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td>
341 </tr>
342 <tr>
343 <td colspan="2" class="size1">Secondary structure Prediction. Winner of Critical Assessment of Protein Structure Prediction 1998 (CASP3). Correct upto 77%. Input type-protein sequence. Required option- <b>email address</b>.</td>
344 </tr>
345 </table>
346 </div>
347 <div id="scanprositedescription" class="description">
348 <table border="0" cellpadding="0" cellspacing="0" width="204">
349 <tr>
350 <td class="size2"><img height="8" width="8" src="images/redear.png"><font color="#cc0000"><b>ScanProsite</b></font></td>
351 <td align="right"><a href="http://us.expasy.org/tools/scanprosite/" target="_blank"><img height="12" width="32" border="0" src="images/more_grey.png"></a></td>
352 </tr>
353 <tr height="1">
354 <td bgcolor="#cccccc" height="1" colspan="2"><spacer type="block" width="32" height="1"></td>
355 </tr>
356 <tr>
357 <td colspan="2" class="size1">Search for PROSITE pattern in your protein sequence. Input type-protein sequence. Required option-none.</td>
358 </tr>
359 </table>
360 </div>
361 <!--Do not edit this tag-->
362 <!--Section #4 and #5 goes here-->
363 </body>
364
365 </html>