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root/SeWeR/sewer_tools.htm
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="generator" content="Adobe GoLive 4">
6 <title>SeWeR: Tools</title>
7 <meta name="author" content="Dr Malay K Basu">
8 <script language="JavaScript" src="scripts/browser.js"></script>
9 <script language="JavaScript1.2"><!--
10 function complement(){
11 str=document.form1.elements[0].value
12 re=/[atgcn]/gi
13 strarray=new Array();
14 if((str!="")||(str!=null)){
15 ch=document.choice.select[document.choice.select.selectedIndex].value
16 var strand2="";
17 strarray=str.match(re);
18
19 if(ch=="inverse"){
20 strarray.reverse();
21 for(i=0;i<strarray.length;i++){
22 if((strarray[i]=="A")||(strarray[i]=="a")){strand2 +="T"}
23 if((strarray[i]=="G")||(strarray[i]=="g")){strand2 +="C"}
24 if((strarray[i]=="T")||(strarray[i]=="t")){strand2 +="A"}
25 if((strarray[i]=="C")||(strarray[i]=="c")){strand2 +="G"}
26 if((strarray[i]=="N")||(strarray[i]=="n")){strand2 +="N"}
27 }}
28 if(ch=="clean"){
29 for(i=0;i<strarray.length;i++){
30 if((strarray[i]=="A")||(strarray[i]=="a")){strand2 +="A"}
31 if((strarray[i]=="G")||(strarray[i]=="g")){strand2 +="G"}
32 if((strarray[i]=="T")||(strarray[i]=="t")){strand2 +="T"}
33 if((strarray[i]=="C")||(strarray[i]=="c")){strand2 +="C"}
34 if((strarray[i]=="N")||(strarray[i]=="n")){strand2 +="N"}
35 }
36 }
37 if(document.choice.checkbox.checked){
38 strand2=strand2.toLowerCase()
39 }
40 document.form2.textfield2.value=strand2
41 }
42 }
43 function clear(){
44 document.form1.elements[0].value="";
45 }
46 function selectresult(){
47
48 document.form2.textfield2.select();
49 document.form2.textfield2.focus();
50
51 }
52 // -->
53 </script>
54 </head>
55
56 <body bgcolor="white" topmargin="0" leftmargin="0" marginheight="0" marginwidth="0" alink="#cc0000" vlink="#cc0000" link="#cc0000">
57 <table border="0" cellpadding="0" cellspacing="0" width="500">
58 <tr height="11">
59 <td width="10" height="11" bgcolor="#cc0000">&nbsp;</td>
60 <td width="10" height="11">&nbsp;</td>
61 <td height="11"><spacer type="block" width="32" height="5"></td>
62 </tr>
63 <tr>
64 <td width="10" rowspan="2" bgcolor="#cc0000"><spacer type="block" width="10" height="32"></td>
65 <td width="10">&nbsp;</td>
66 <td><img height="39" width="68" src="images/sewer_logo_small.png"></td>
67 </tr>
68 <tr>
69 <td width="10">&nbsp;</td>
70 <td>
71 <table border="0" cellpadding="0" cellspacing="0" width="482">
72 <tr height="5">
73 <td height="5" colspan="2"><spacer type="block" width="32" height="5"></td>
74 </tr>
75 <tr height="1">
76 <td height="1" colspan="2" bgcolor="#cc0000"><spacer type="block" width="32" height="1"></td>
77 </tr>
78 <tr>
79 <form name="choice">
80
81 <td class="size1" width="221"><select name="select" size="1">
82 <option value="inverse" selected>Inverse complement
83 <option value="clean">Clean Sequence
84 </select></td>
85 <td align="center" class="size1" width="261"><input type="checkbox" name="checkbox" value="lower"> <b>All lowercase</b></td>
86 </form>
87 </tr>
88 <tr>
89 <form name="form1">
90
91 <td colspan="2" class="size1"><img height="8" width="8" src="images/redear.png"><b>Query Sequence Box<br>
92 </b><textarea name="textfield" cols="50" wrap="virtual" rows="5"></textarea></td>
93 </form>
94 </tr>
95 <tr>
96 <td width="221"><a href="javascript:complement()"><img height="18" width="69" border="0" src="images/submit.png"></a></td>
97 <td width="261"><a href="javascript:clear()"><img height="15" width="35" border="0" src="images/clear.png"></a></td>
98 </tr>
99 <tr height="1">
100 <td height="1" colspan="2" bgcolor="#cc0000"><spacer type="block" width="32" height="1"></td>
101 </tr>
102 <tr height="20">
103 <td width="221" height="20"><spacer type="block" width="32" height="20"></td>
104 <td height="20" width="261"></td>
105 </tr>
106 <tr height="1">
107 <form name="form2">
108
109 <td height="1" colspan="2" class="size1"><img height="8" width="8" src="images/redear.png"><b>Result</b><br>
110 <textarea name="textfield2" cols="50" wrap="virtual" rows="5"></textarea></td>
111 </form>
112 </tr>
113 <tr>
114 <td colspan="2" class="size1" align="right"><br>
115 <a href="javascript:selectresult()"><img src="images/selectall.png" border="0" width="67" height="13"></a><br>
116 <hr noshade size="1">
117 </td>
118 </tr>
119 <tr height="1" align="left">
120 <td height="1" colspan="2" class="body">
121 <div align="left">
122 <ul type="square">
123 <li>Paste a DNA sequence in <b>Query Sequence Box</b>
124 <li>Choose the action to perform on the sequence. You can <b>Inverse-complement</b> the sequence or <b>Clean</b> the sequence. In either case <font color="#cc0000">SeWeR</font> will filter out only A/T/G/C/N from the query. <b>All spaces, numbers, line-breaks will be removed from the sequence</b>
125 <li><b>The result will appear in the Result Box</b>
126 </ul>
127 </div>
128 </td>
129 </tr>
130 <tr height="1">
131 <td height="1" colspan="2">
132 <hr noshade size="1">
133 </td>
134 </tr>
135 <tr height="1">
136 <td height="1" colspan="2" class="size1"><font color="#666666">Copyright &copy; 2000, 2003, 2004 Malay K Basu</font><br>
137 <a href="mailto:malay@bioinformatics.org">malay@bioinformatics.org</a></td>
138 </tr>
139 <tr height="1">
140 <td height="1" colspan="2">&nbsp;</td>
141 </tr>
142 </table>
143 </td>
144 </tr>
145 </table>
146 </body>
147
148 </html>