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Revision: 1.1.1.1 (vendor branch)
Committed: Mon Aug 23 19:36:27 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 <title>SeWeR: Sequence Alignment</title>
7 <!--Do not edit this tag-->
8 <!--Section #1 code goes here-->
9 <!--included_programs="clustalw,blockmaker"-->
10 <!--Section #1 code goes here-->
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
16 function init(){
17 if(isNS6){
18 document.all=document.getElementsByTagName("*");
19 }
20 program=new Array();
21 option=new Array();
22 description=new Array();
23 program[0]=new ProgramConstructor("clustalw","http://clustalw.genome.ad.jp/","http://clustalw.genome.ad.jp/sit-bin/nph-clustalw","http://clustalw.genome.ad.jp/SIT/clustalw_help.html","sequence","post","multipart/form-data");
24 program[1]=new ProgramConstructor("blockmaker","http://blocks.fhcrc.org/blocks/blockmkr/make_blocks.html","http://blocks.fhcrc.org/blockmkr-bin/makeblocks.pl","http://blocks.fhcrc.org/blocks/blockmkr/help/help.html","sequences","POST","multipart/form-data");
25
26 option[0]=new makeOption("clustalw");
27 option[1]=new makeOption("blockmaker");
28
29 description[0]=new makeDescription("clustalw");
30 description[1]=new makeDescription("blockmaker");
31
32 /*********************************************************************
33 ******************** CUSTOMIZATION CODE *****************************
34 **********************************************************************/
35 /*Do not edit this tag*/
36 /**Section #2 code goes here**/
37
38 for(i=0;i<option.length;i++){
39 option[i].hideit();
40 }
41 writeprogrambanner();
42 showDescription();
43 }
44 </script>
45
46
47 </head>
48
49 <body bgcolor="white" topmargin="0" leftmargin="0" marginheight="0" marginwidth="0" alink="#cc0000" vlink="#cc0000" link="#cc0000" onload="init(), genjob()">
50 <table border="0" cellpadding="0" cellspacing="0">
51 <tr>
52 <td bgcolor="#cc0000" width="10"><spacer type="block" width="10" height="32"></td>
53 <td width="528">
54 <table border="0" cellpadding="0" cellspacing="0" width="522">
55 <tr height="20">
56 <td width="20" height="20">&nbsp;</td>
57 <td height="20">&nbsp;</td>
58 </tr>
59 <tr>
60 <td width="20"></td>
61 <td><img height="21" width="268" src="images/alignment.png"></td>
62 </tr>
63 <tr height="20">
64 <td width="20" height="20"></td>
65 <td height="20"></td>
66 </tr>
67 <tr height="20">
68 <td width="20" height="20"></td>
69 <td class="body" height="20">
70 <table width="436" border="0" cellspacing="0" cellpadding="0" mm_noconvert="TRUE" height="190">
71 <tr>
72 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
73 <form name="programchoice">
74
75 <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()">
76 <option value="clustalw" selected>ClustalW
77 <option value="blockmaker">Block Maker
78 <!--Do not edit this tag-->
79 <!--Section #3 code goes here-->
80 </select></td>
81 </form>
82
83 <td class="size1" bgcolor="#cccccc" colspan="2" valign="middle" align="right">
84 <div align="right">
85 <a href="javascript:check('submit')"><img src="images/submit.png" width="69" height="18" border="0" alt="Submit query"></a></div>
86 </td>
87 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
88 </tr>
89 <tr>
90 <td class="size1" bgcolor="#cccccc" colspan="4"><img src="images/query.png" width="47" height="17"></td>
91 </tr>
92 <tr>
93 <form name="query" onsubmit="javascript:check()">
94
95 <td class="size1" bgcolor="#e6e6e6" colspan="4" align="center" valign="middle"><textarea name="textfield" cols="50" rows="5"></textarea></td>
96 </form>
97 </tr>
98 <tr>
99 <td bgcolor="#cccccc" colspan="4"><spacer type="block" width="1" height="1"></td>
100 </tr>
101 <tr height="5">
102 <td bgcolor="white" height="5" width="86"><spacer type="block" width="1" height="5"></td>
103 <td bgcolor="white" height="5">&nbsp;</td>
104 <td bgcolor="white" align="right" height="5">&nbsp;</td>
105 <td bgcolor="white" align="right" height="5">&nbsp;</td>
106 </tr>
107 <tr>
108 <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>
109 <td bgcolor="white" align="left"><a href="javascript:check('customize')"><img border="0" height="10" width="56" src="images/customize.png"></a></td>
110 <td bgcolor="white"><a href="javascript:clearForm()"><img src="images/clear.png" width="35" height="15" border="0" alt="Clear this form"></a></td>
111 <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>
112 </tr>
113 <tr height="1">
114 <td bgcolor="#cccccc" colspan="4" height="1"><spacer type="block" width="1" height="1"></td>
115 </tr>
116 </table>
117 <table border="0" cellpadding="0" cellspacing="0" width="435" height="197">
118 <tr>
119 <td class="body" valign="middle">
120 <ul type="square">
121 <li>Select the <b>program</b> of choice.
122 <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.
123 <li>Click <b>Options button</b> to fill up options. The button is a toggle. Clicking it again will close the option.
124 <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.
125 <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.
126 <li>Click <b>Submit</b> to pass on the query. SeWeR will open a new window for results.
127 </ul>
128 </td>
129 </tr>
130 </table>
131 </td>
132 </tr>
133 <tr height="1">
134 <td height="1" colspan="2" bgcolor="#cc0000"><spacer type="block" width="32" height="1"></td>
135 </tr>
136 <tr height="20">
137 <td width="20" height="20"></td>
138 <td height="20"><spacer type="block" width="32" height="20"></td>
139 </tr>
140 <tr height="1">
141 <td width="20" height="1"></td>
142 <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>
143 <p><a href="copyright.htm"><font color="#666666">Copyright </font></a><font color="#666666">&copy; 2000, 2003 Malay Kumar Basu<br>
144 Send your comments/suggestions/bug-report to me:<br>
145 <a href="mailto:malay@bioinformatics.org">malay@bioinformatics.org</a><br>
146 <a href="copyright.htm">Disclaimer</a></font><br>
147 <br>
148 </td>
149 </tr>
150 </table>
151 </td>
152 <td width="1" bgcolor="#cc0000"><spacer type="block" width="1" height="32"></td>
153 </tr>
154 </table>
155
156 <div id="programbanner"><p class="heading">Program Name</p>
157 </div>
158 <div id="result"></div>
159 <div id="sewer"><img height="39" width="68" border="0" src="images/sewer_logo_small.png"></div>
160 <div id="clustalw" class="optionlist">
161 <form name="clustalwform">
162 <table width="600" border="0" bgcolor="#e6e6e6" cellpadding="5" cellspacing="5">
163 <tr><td class="size1"><p class="size2"><font color="#cc0000"><b>clustalw</b></font></p>
164 <p><b>Output format </b> <select name="output">
165 <option selected value=" ">CLUSTAL
166 <option value="gcg">GCG(MSF)
167 <option value="gde">GDE
168 <option value="pir">PIR
169 <option value="phylip">Phylip
170 </select><p><b>Pairwise Alignment </b>
171 <input type="radio" name="pwalignment" value="fast" checked>
172 <b>Fast/approximate</b>
173 <input type="radio" name="pwalignment" value="slow">
174 <b>Slow/Accurate</b><p>
175
176 <hr noshade size="1">
177 <span class="size2"><font color="#cc0000"><b>Pairwise alignment parameters for fast/approximate</b></font></span><p>
178 <b>K-tuple(word) size</b>
179 <input type="text" size="15" name="ktuple" value="1">
180 <p><b>Window size</b>
181 <input type="text" size="15" name="window" value="5">
182 <p><b>Gap Penalty</b>
183 <input type="text" size="15" name="pairgap" value="3">
184 <p><b>Number of Top Diagonals</b>
185 <input type="text" size="15" name="topdiags" value="5"><p><b>Scoring Method</b> <select name="score">
186 <option selected value="percent">PERCENT
187 <option value="absolute">ABSOLUTE
188 </select>
189
190 <hr noshade size="1">
191 <span class="size2"><font color="#cc0000"><b>Pairwise alignment parameters for slow/accurate</b></font></span><p>
192
193 <p><b>Gap Open Penalty</b>
194 <input type="text" size="15" name="pwgapopen" value="10.0">
195 <p><b>Gap Extension Penalty</b>
196 <input type="text" size="15" name="pwgapext" value="0.1"><p><b>Weight Matrix</b> <select name="pwmatrix">
197 <option selected value="blosum">BLOSUM (for PROTEIN)
198 <option value="pam">PAM (for PROTEIN)
199 <option value="gonnet">GONNET (for PROTEIN)
200 <option value="id">ID (for PROTEIN)
201 <option value="iub">IUB (for DNA)
202 <option value="clustalw">CLUSTALW (for DNA)
203 </select>
204
205 <hr noshade size="1">
206 <span class="size2"><font color="#cc0000"><b>Multiple alignment parameters</b></font></span><p>
207
208 <p><b>Gap Open Penalty</b>
209 <input type="text" size="15" name="gapopen" value="10">
210 <p><b>Gap Extension Penalty</b>
211 <input type="text" size="15" name="gapext" value="0.05"><p>
212 <b>Weight Transition</b><input type="radio" name="transitions" value="Yes">
213 <b>Yes</b> <input type="radio" name="transitions" value="No" checked>
214 <b>No</b><p><b>Weight transition value</b>
215 <input type="text" size="15" name="trans_weight" value="0.5"><p>
216 <p><b>Hydrophilic Residues for Proteins</b>
217 <input type="text" size="15" name="hgapresidues" value="GPSNDQERK"><p>
218 <b>Hydrophilic Gaps</b>
219 <input type="radio" name="nohgap" value="Yes" checked>
220 <b>Yes</b>
221 <input type="radio" name="nohgap" value="No">
222 <b>No</b><p><b>Weight Matrix</b> <select name="matrix">
223 <option selected value="blosum">BLOSUM (for PROTEIN)
224 <option value="pam">PAM (for PROTEIN)
225 <option value="gonnet">GONNET (for PROTEIN)
226 <option value="id">ID (for PROTEIN)
227 <option value="iub">IUB (for DNA)
228 <option value="clustalw">CLUSTALW (for DNA)
229 </select>
230 <p><b>Additional options (delimited by whitespaces)</b>
231 <input type="text" size="15" name="other_param" value="">
232 <input type="hidden" name="service" value="clustalw"></td></tr></table>
233 </form></div>
234
235
236 <div id="blockmaker" class="optionlist">
237 <form name="blockmakerform">
238 <table width="600" border="0" cellpadding="10" bgcolor="#e6e6e6" cellspacing="0">
239 <tr>
240 <td class="size3" width="269"><font color="#cc0000"><b>block maker</b></font></td>
241 <td width="315">&nbsp;</td>
242 </tr>
243 <tr>
244 <td class="size1" width="269"><b>Your email</b> <input size="30" name="address" type="text"></td>
245 <td class="size1" width="315"><b>Sequence Description</b> <input size="20" name="desc" type="text"></td>
246 </tr>
247 </table>
248 </form>
249 </div>
250
251 <div id="clustalwdescription" class="description">
252 <table border="0" cellpadding="0" cellspacing="0" width="204">
253 <tr>
254 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>ClustalW</b></td>
255 <td align="right"><a href="http://clustalw.genome.ad.jp/" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
256 </tr>
257 <tr><td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td></tr><tr><td colspan="2" class="size1">At Kyoto university bioinformatics center. Align multiple sequence. Input type, DNA or protein sequences. See help to find out the input format of the sequences. Required option, none.</td></tr></table>
258 </div>
259 <div id="blockmakerdescription" class="description">
260 <table border="0" cellpadding="0" cellspacing="0" width="204">
261 <tr>
262 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>Block Maker</b></td>
263 <td align="right"><a href="http://blocks.fhcrc.org/blocks/blockmkr/make_blocks.html" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
264 </tr>
265
266 <tr height="1">
267 <td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td>
268 </tr>
269
270 <tr>
271 <td class="size1" colspan="2">At Fred Hutchinson Cancer Research Center. Finds conserved blocks in a group of two or more unaligned protein sequences. At least two protein sequences must be provided
272 to make blocks. Each sequence must have a unique name of 10 characters or less. All sequences must be of same format (FASTA). Input type- protein sequences. <b>Required option- email for 25 sequences
273 or more than 15,000 amino acids</b>.</td>
274 </tr>
275 </table>
276 </div>
277 <!--Do not edit this tag-->
278 <!--Section #4 and #5 goes here-->
279 </body>
280
281 </html>