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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 <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="pubmed,blocks,blastp,blastn,blastx"-->
8 <!--Section #1 code goes here-->
9 <title>SeWeR: Database Searches</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 if(isNS6){
17 document.all=document.getElementsByTagName("*");
18 }
19 program=new Array();
20 program[0]=new ProgramConstructor("pubmed","http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed","http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?SUBMIT=y","http://www.ncbi.nlm.nih.gov:80/entrez/query/static/help/pmhelp.html","term","post","application/x-www-form-urlencoded");
21 program[1]=new ProgramConstructor("blocks","http://blocks.fhcrc.org/blocks/blocks_search.html","http://blocks.fhcrc.org/blocks-bin/blocks_search","http://blocks.fhcrc.org/blocks/help/help.html","sequence","post","application/x-www-form-urlencoded");
22
23 program[2]=new ProgramConstructor("blastp","http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=Proteins&PROGRAM=blastp","http://www.ncbi.nlm.nih.gov/blast/Blast.cgi","http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html","QUERY","post","application/x-www-form-urlencoded");
24
25 option=new Array();
26 option[0]=new makeOption("blastp");
27 option[1]=new makeOption("pubmed")
28 option[2]=new makeOption("blocks")
29
30
31 description=new Array();
32 description[0]=new makeDescription("blastp");
33 description[1]=new makeDescription("pubmed");
34 description[2]=new makeDescription("blocks");
35
36
37 /*********************************************************************
38 ******************** CUSTOMIZATION CODE *****************************
39 **********************************************************************/
40 /*Do not edit this tag*/
41
42
43
44
45 program[3]=new ProgramConstructor("blastn","http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn","http://www.ncbi.nlm.nih.gov/blast/Blast.cgi","http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html","QUERY","post","application/x-www-form-urlencoded");
46 option[3]=new makeOption("blastn");
47 description[3]=new makeDescription("blastn");
48
49 program[4]=new ProgramConstructor("translate_blast","http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=Translations&PROGRAM=blastx","http://www.ncbi.nlm.nih.gov/blast/Blast.cgi","http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html","QUERY","post","application/x-www-form-urlencoded");
50 option[4]=new makeOption("translate_blast");
51 description[4]=new makeDescription("translate_blast");
52
53 /**Section #2 code goes here**/
54
55
56
57
58 for(i=0;i<option.length;i++){
59 option[i].hideit();
60 }
61 writeprogrambanner();
62 showDescription();
63 }
64 </script>
65
66
67 </head>
68
69 <body bgcolor="white" topmargin="0" leftmargin="0" marginheight="0" marginwidth="0" alink="#cc0000" vlink="#cc0000" link="#cc0000" onload="init()">
70 <table border="0" cellpadding="0" cellspacing="0">
71 <tr>
72 <td bgcolor="#cc0000" width="10"><spacer type="block" width="10" height="32"></td>
73 <td width="528">
74 <table border="0" cellpadding="0" cellspacing="0" width="522">
75 <tr height="20">
76 <td width="20" height="20">&nbsp;</td>
77 <td height="20">&nbsp;</td>
78 </tr>
79 <tr>
80 <td width="20"></td>
81 <td><img height="20" width="268" src="images/databasearch.png"></td>
82 </tr>
83 <tr height="20">
84 <td width="20" height="20"></td>
85 <td height="20"></td>
86 </tr>
87 <tr height="20">
88 <td width="20" height="20"></td>
89 <td class="body" height="20">
90 <table width="436" border="0" cellspacing="0" cellpadding="0" mm_noconvert="TRUE" height="190">
91 <tr>
92 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
93 <form name="programchoice">
94
95 <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()">
96 <option value="blastn" selected>BLASTN
97 <option value="blastp">BLASTP
98
99 <option value="translate_blast">Translated BLAST
100 <option value="blocks">Blocks Searcher
101
102 <option value="pubmed">PubMed
103
104
105 <!--Do not edit this tag-->
106
107
108 <!--Section #3 code goes here-->
109
110
111
112 </select></td>
113 </form>
114
115 <td class="size1" bgcolor="#cccccc" colspan="2" valign="middle" align="right">
116 <div align="right">
117 <a href="javascript:check('submit')"><img src="images/submit.png" width="69" height="18" border="0" alt="Submit query"></a></div>
118 </td>
119 <td class="size1" rowspan="7" bgcolor="#cccccc" width="1"><spacer type="block" width="1" height="1"></td>
120 </tr>
121 <tr>
122 <td class="size1" bgcolor="#cccccc" colspan="4"><img src="images/query.png" width="47" height="17"></td>
123 </tr>
124 <tr>
125 <form name="query" onsubmit="javascript:check()">
126
127 <td class="size1" bgcolor="#e6e6e6" colspan="4" align="center" valign="middle"><textarea name="textfield" cols="50" rows="5"></textarea></td>
128 </form>
129 </tr>
130 <tr>
131 <td bgcolor="#cccccc" colspan="4"><spacer type="block" width="1" height="1"></td>
132 </tr>
133 <tr height="5">
134 <td bgcolor="white" height="5" width="86"><spacer type="block" width="1" height="5"></td>
135 <td bgcolor="white" height="5">&nbsp;</td>
136 <td bgcolor="white" align="right" height="5">&nbsp;</td>
137 <td bgcolor="white" align="right" height="5">&nbsp;</td>
138 </tr>
139 <tr>
140 <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>
141 <td bgcolor="white" align="left"><a href="javascript:check('customize')"><img border="0" height="10" width="56" src="images/customize.png"></a></td>
142 <td bgcolor="white"><a href="javascript:clearForm()"><img src="images/clear.png" width="35" height="15" border="0" alt="Clear this form"></a></td>
143 <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>
144 </tr>
145 <tr height="1">
146 <td bgcolor="#cccccc" colspan="4" height="1"><spacer type="block" width="1" height="1"></td>
147 </tr>
148 </table>
149 <table border="0" cellpadding="0" cellspacing="0" width="435" height="197">
150 <tr>
151 <td class="body" valign="middle">
152 <ul type="square">
153 <li>Select the <b>program</b> of choice.
154 <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.
155 <li>Click <b>Options button</b> to fill up options. The button is a toggle. Clicking it again will close the option.
156 <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.
157 <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.
158 <li>Click <b>Submit</b> to pass on the query. SeWeR will open a new window for results.
159 </ul>
160 </td>
161 </tr>
162 </table>
163 </td>
164 </tr>
165 <tr height="1">
166 <td height="1" colspan="2" bgcolor="#cc0000"><spacer type="block" width="32" height="1"></td>
167 </tr>
168 <tr height="20">
169 <td width="20" height="20"></td>
170 <td height="20"><spacer type="block" width="32" height="20"></td>
171 </tr>
172 <tr height="1">
173 <td width="20" height="1"></td>
174 <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>
175 <p><a href="copyright.htm"><font color="#666666">Copyright </font></a><font color="#666666">&copy; 2000, 2003, 2004 Malay Kumar Basu<br>
176 Send your comments/suggestions/bug-report to me:<br>
177 <a href="mailto:malay@bioinformatics.org">malay@bioinformatics.org</a><br>
178 <a href="copyright.htm">Disclaimer</a></font><br>
179 <br>
180 </td>
181 </tr>
182 </table>
183 </td>
184 <td width="1" bgcolor="#cc0000"><spacer type="block" width="1" height="32"></td>
185 </tr>
186 <tr height="600">
187 <td><spacer type="block" width="1" height="600"></td>
188 </tr>
189 </table>
190
191 <div id="programbanner"><p class="heading">Program Name</p></div>
192 <div id="result"></div>
193 <div id="sewer"><img height="39" width="68" border="0" src="images/sewer_logo_small.png"></div>
194
195
196 <div id="pubmed" class="optionlist">
197 <form name="pubmedform">
198 <table width="608" border="0" cellspacing="0" cellpadding="10" bgcolor="#e6e6e6">
199 <tr height="22">
200 <td colspan="2" class="size2" height="22"><font color="#cc0000"><b>pubmed</b></font></td>
201 </tr>
202 <tr>
203 <td width="280" class="size1"><b>Field</b> <select name="defaultField" size="1">
204 <option value="Affiliation">Affiliation
205 <option selected value="All Fields">All Fields
206 <option value="Author Name">Author Name
207 <option value="EC/RN Number">EC/RN Number
208 <option value="Entrez Date">Entrez Date
209 <option value="Filter">Filter
210 <option value="Issue">Issue
211 <option value="Journal Name">Journal Name
212 <option value="Language">Language
213 <option value="MeSH Date">MeSH Date
214 <option value="MeSH Major Topic">MeSH Major Topic
215 <option value="MeSH Terms">MeSH Terms
216 <option value="Page Number">Page Number
217 <option value="Publication Date">Publication Date
218 <option value="Publication Type">Publication Type
219 <option value="Secondary Source ID">Secondary Source ID
220 <option value="Subheading">Subheading
221 <option value="Substance Name">Substance Name
222 <option value="Text Word">Text Word
223 <option value="Title Word">Title Word
224 <option value="UID">UID
225 <option value="Volume">Volume
226 </select></td>
227 <td width="282" class="size1"><input name="pmfilter_HasAbstract" type="checkbox" value="only items with abstracts"> <b>only items with abstracts&nbsp; </b></td>
228 </tr>
229 <tr height="47">
230 <td class="size1" width="280" height="47"><b>Publication Type</b> <select name="pmfilter_PubType" size="1">
231 <option selected value="">
232 <option value="">Clinical Trial
233 <option value="">Editorial
234 <option value="">Letter
235 <option value="">Meta-Analysis
236 <option value="">Practice Guideline
237 <option value="">Randomized Controlled Trial
238 <option value="">Review
239 </select></td>
240 <td class="size1" width="282" height="47"><b>Language</b> <select name="pmfilter_Language" size="1">
241 <option selected value="">
242 <option value="">English
243 <option value="">French
244 <option value="">German
245 <option value="">Italian
246 <option value="">Japanese
247 <option value="">Russian
248 <option value="">Spanish
249 </select></td>
250 </tr>
251 <tr height="47">
252 <td class="size1" width="280" height="47"><b>Entrez date</b> <select name="pmfilter_EDatLimit" size="1">
253 <option value="">
254 <option value="">30 Days
255 <option value="">60 Days
256 <option value="">90 Days
257 <option value="">180 Days
258 <option value="">1 Year
259 <option value="">2 Years
260 <option value="">5 Years
261 <option value="">10 Years
262 </select></td>
263 <td class="size1" width="282" height="47"><b>Subsets</b> <select name="pmfilter_Subsets" size="1">
264 <option value="">
265 <option value="">AIDS
266 <option value="">AIM
267 <option value="">Dental
268 <option value="">MEDLINE
269 <option value="">Nursing
270 <option value="">PreMEDLINE
271 <option value="">Publisher
272 <option value="">PubRef
273 </select></td>
274 </tr>
275 <tr>
276 <td class="size1" colspan="2"><b>Date</b> <select name="pmfilter_DateRange_Field" size="1">
277 <option value="">
278 <option value="">Publication Date
279 <option value="">Entrez Date
280 </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>
281 Use the format YYYY/MM/DD; month and day are optional.</td>
282 </tr>
283 </table>
284 <input name="db" type="hidden" value="PubMed"> <input name="orig_db" type="hidden" value="PubMed"> <input name="cmd" type="hidden" value="search">
285 </form>
286 </div>
287
288 <div id="blocks" class="optionlist">
289 <form name="blocksform">
290 <table width="600" border="0" cellspacing="0" cellpadding="10" bgcolor="#e6e6e6">
291 <tr height="31">
292 <td colspan="2" height="31" class="size2"><font color="#cc0000"><b>blocks search</b></font></td>
293 <td width="299" height="31"></td>
294 </tr>
295 <tr height="23">
296 <td width="257" height="23" class="size1"><b>Email (optional)</b> <input size="25" name="address" type="text"></td>
297 <td width="299" height="23" class="size1"><b>Database </b><select name="database" size="1">
298 <option value="plus" selected>Blocks+
299 <option value="minus">Blocks+ without compositionally biased blocks
300 <option value="prints">Prints Database in blocks format
301 </select></td>
302 <td width="299" height="23"></td>
303 </tr>
304 <tr height="10">
305 <td width="257" height="10" class="size1"><b>Cutoff expected value</b> <select name="ex" size="1">
306 <option value="1">1
307 <option value="2">2
308 <option value="3">3
309 <option value="4">4
310 <option value="5" selected>5
311 <option value="6">6
312 <option value="7">7
313 <option value="8">8
314 <option value="9">9
315 <option value="10">10
316 </select></td>
317 <td width="299" height="10" class="size1"><b>Amount of output</b> <select name="ou" size="1">
318 <option value="all" selected>Summary with alignments
319 <option value="sum">Summary only
320 <option value="gff">GFF format
321 <option value="old">Old style results
322 <option value="raw">Raw results only
323 </select></td>
324 <td width="299" height="10"></td>
325 </tr>
326 <tr height="2">
327 <td colspan="2" height="2" class="size1"><b>Sequence type</b> <select name="ty" size="1">
328 <option value="auto" selected>Determine automatically
329 <option value="AA">Amino acid
330 <option value="DNA">DNA
331 </select></td>
332 <td width="299" height="2"></td>
333 </tr>
334 <tr height="2">
335 <td colspan="2" height="2" class="size1"><font color="#cc0000"><b>For DNA Query</b></font><br>
336 <hr size="1" noshade>
337 </td>
338 <td width="299" height="2"></td>
339 </tr>
340 <tr height="2">
341 <td width="257" height="2" class="size1"><b>Strands to search</b> <select name="st" size="1">
342 <option value="2" selected>Both
343 <option value="1">Forward only
344 <option value="-1">Reverse only
345 </select></td>
346 <td width="299" height="2" class="size1"><b>Genetic code</b> <select name="ge" size="1">
347 <option value="0" selected>Standard
348 <option value="1">Vertebrate Mitochondrial
349 <option value="2">Yeast Mitochondrial
350 <option value="3">Mold Mitochondrial and Mycoplasma
351 <option value="4">Invertebrate Mitochondrial
352 <option value="5">Ciliate Macronuclear
353 <option value="6">Protozoan Mitochondrial
354 <option value="7">Plant Mitochondrial
355 <option value="8">Echinodermate Mitochondrial
356 </select></td>
357 <td width="299" height="2"></td>
358 </tr>
359 </table>
360 </form>
361 </div>
362
363
364
365 <div id="pubmeddescription" class="description">
366 <table border="0" cellpadding="0" cellspacing="0" width="204">
367 <tr>
368 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>PubMed</b></td>
369 <td align="right"><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
370 </tr>
371 <tr height="1">
372 <td colspan="2" bgcolor="#cccccc" height="1"><spacer type="block" width="32" height="1"></td>
373 </tr>
374 <tr>
375 <td colspan="2" class="size1">Search bibliographic database at NCBI. Input type-key-word. Can accept boolean search. Required option-none.</td>
376 </tr>
377 </table>
378 </div>
379 <div id="blocksdescription" class="description">
380 <table border="0" cellpadding="0" cellspacing="0" width="204">
381 <tr>
382 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>Blocks Searcher</b></td>
383 <td align="right"><a href="http://blocks.fhcrc.org/blocks/blocks_search.html" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
384 </tr>
385 <tr height="1">
386 <td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td>
387 </tr>
388 <tr>
389 <td colspan="2" class="size1">Search BLOCKS database for similarity. Input type- protein or DNA sequence. Required options-none.</td>
390 </tr>
391 </table>
392 </div>
393
394 <!--Do not edit this tag-->
395 <div id="blastpdescription" class="description">
396 <table border="0" cellpadding="0" cellspacing="0" width="204">
397 <tr>
398 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>BLASTP</b></td>
399 <td align="right"><a href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=Proteins&PROGRAM=blastp" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
400 </tr>
401 <tr><td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td></tr><tr><td colspan="2" class="size1">Search a protein sequence against the protein sequences on NCBI server. Query type-<b>Protein Sequence</b>. Required option- <b>none</b></td></tr></table>
402 </div><div id="blastp" class="optionlist">
403 <form name="blastpform">
404 <table width="600" border="0" bgcolor="#e6e6e6" cellpadding="5" cellspacing="5">
405 <tr><td class="size1"><p class="size2"><font color="#cc0000"><b>blastp</b></font></p>
406
407 <p><b>Set subsequence: From </b>
408 <input type="text" size="15" name="QUERY_FROM" value="">
409 <b>To </b>
410 <input type="text" size="15" name="QUERY_TO" value=""><p><b>Database</b> <select name="DATABASE">
411 <option selected >nr
412 <option >swissprot
413 <option >prat
414 <option >yeast
415 <option >ecoli
416 <option >pdb
417 <option >Drosophila genome
418 <option >month
419 </select>
420 <input type="checkbox" name="CDD_SEARCH" value="on" checked>
421 <b>Do CD-search</b>
422 <hr noshade size="1">
423 <p><b>Limit by Entrez query</b>
424 <input type="text" size="15" name="ENTREZ_QUERY" value=""><p><b>or select from</b> <select name="ENTREZ_QUERY">
425 <option selected >(none)
426 <option >Viruses [ORGN]
427 <option >Archaea [ORGN]
428 <option >Bacteria [ORGN]
429 <option >Eukaryota [ORGN]
430 <option >Viridiplantae [ORGN]
431 <option >Fungi [ORGN]
432 <option >Metazoa [ORGN]
433 <option >Arthropoda [ORGN]
434 <option >Vertebrata [ORGN]
435 <option >Mammalia [ORGN]
436 <option >Rodentia [ORGN]
437 <option >Primates [ORGN]
438 <option >-------------------
439 <option >Aeropyrum pernix [ORGN]
440 <option >Aquifex aeolicus [ORGN]
441 <option >Arabidopsis thaliana [ORGN]
442 <option >Bacillus subtilis [ORGN]
443 <option >Bos taurus [ORGN]
444 <option >Caenorhabditis elegans [ORGN]
445 <option >Danio rerio [ORGN]
446 <option >Dictyostelium discoideum [ORGN]
447 <option >Drosophila melanogaster [ORGN]
448 <option >Escherichia coli [ORGN]
449 <option >Gallus gallus [ORGN]
450 <option >Homo sapiens [ORGN]
451 <option >Human immunodeficiency virus type 1 [ORGN]
452 <option >Methanococcus jannaschii [ORGN]
453 <option >Mus musculus [ORGN]
454 <option >Oryctolagus cuniculus [ORGN]
455 <option >Oryza sativa [ORGN]
456 <option >Ovis aries [ORGN]
457 <option >Plasmodium falciparum [ORGN]
458 <option >Rattus norvegicus [ORGN]
459 <option >Saccharomyces cerevisiae [ORGN]
460 <option >Schizosaccharomyces pombe [ORGN]
461 <option >Simian immunodeficiency virus [ORGN]
462 <option >Synechocystis PCC6803 [ORGN]
463 <option >Takifugu rubripes [ORGN]
464 <option >Xenopus laevis [ORGN]
465 <option >Zea mays [ORGN]
466 </select><p>
467 <input type="checkbox" name="COMPOSITION_BASED_STATISTICS" value="on" checked>
468 <b>Composition based statistics</b><p><b>Choose Filter: </b><br>
469 <input type="checkbox" name="FILTER" value="L" checked>
470 <b> Low complexity</b>
471 <input type="checkbox" name="FILTER" value="m">
472 <b>Mask for lookup table only</b>
473 <input type="checkbox" name="LCASE_MASK" value="on">
474 <b>Mask lower case</b>
475 <p><b>Expect</b>
476 <input type="text" size="15" name="EXPECT" value="10"><p><b>Word Size</b> <select name="WORD_SIZE">
477 <option >2
478 <option selected >3
479 </select><p><b>Matrix</b> <select name="MATRIX_NAME">
480 <option >PAM30
481 <option >PAM70
482 <option >BLOSUM80
483 <option selected >BLOSUM62
484 <option >BLOSUM45
485 </select><p><b>Gap cost</b> <select name="GAPCOSTS">
486 <option selected >11 1
487 <option >9 2
488 <option >8 2
489 <option >7 2
490 <option >12 1
491 <option >10 1
492 </select>
493 <p><b>PSSM</b><br><textarea name="PSSM" rows="5" cols="50">
494 </textarea>
495 <p><b>Other Advanced option</b>
496 <input type="text" size="15" name="OTHER_ADVANCED" value="">
497 <p><b>PHI pattern</b>
498 <input type="text" size="15" name="PHI_PATTERN" value=""><p>
499 <hr noshade size="1">
500 <input type="checkbox" name="SHOW_OVERVIEW" value="on" checked>
501 <b>Show overview</b>
502 <input type="checkbox" name="NCBI_GI" value="on" checked>
503 <b>NCBI GI</b><p><b>Show</b> <select name="FORMAT_OBJECT">
504 <option selected value="Alignment">Alignment
505 <option value="PSSM">PSSM
506 <option value="Bioseq">Bioseq
507 </select><b>Format</b> <select name="FORMAT_TYPE">
508 <option selected value="HTML">HTML
509 <option value="Text">Plain text
510 <option value="ASN.1">ASN.1
511 <option value="XML">XML
512 </select><p><b>Number of descriptions</b> <select name="DESCRIPTIONS">
513 <option >0
514 <option >10
515 <option >50
516 <option selected >100
517 <option >250
518 <option >500
519 <option >1000
520 </select><p><b>Number of alignments</b> <select name="ALIGNMENTS">
521 <option >0
522 <option >10
523 <option selected >50
524 <option >100
525 <option >250
526 <option >500
527 <option >1000
528 </select><p><b>Alignment view</b> <select name="ALIGNMENT_VIEW">
529 <option selected value="Pairwise">Pairwise
530 <option value="QueryAnchored">query-anchored with identities
531 <option value="QueryAnchoredNoIdentities">query-anchored without identities
532 <option value="FlatQueryAnchored">flat query-anchored with identities
533 <option value="FlatQueryAnchoredNoIdentities">flat query-anchored without identities
534 </select><p>
535 <input type="checkbox" name="RUN_PSIBLAST" value="on">
536 <b>Format for PSI-BLAST</b>
537 <b> with inclusion threshhold</b>
538 <input type="text" size="15" name="I_THRESH" value="0.001"><p><b>Layout</b> <select name="LAYOUT">
539 <option value="OneWindow">One Window
540 <option selected value="TwoWindows">Two Windows
541 </select><p><b>Format on the result page</b> <select name="FORMAT_BLOCK_ON_RESPAGE">
542 <option selected value="None">None
543 <option value="Top">At the top
544 <option value="Bottom">At the bottom
545 </select><p><b>Autoformat</b> <select name="AUTO_FORMAT">
546 <option value="Off">Off
547 <option selected value="Semiauto">Semi-auto
548 <option value="Fullauto">Full-auto
549 </select>
550 <p><b>Send result by e. mail</b>
551 <input type="text" size="15" name="EMAIL_ADDRESS" value="">
552 <input type="hidden" name="PROGRAM" value="blastp">
553 <input type="hidden" name="CLIENT" value="web">
554 <input type="hidden" name="SERVICE" value="plain">
555 <input type="hidden" name="PAGE" value="Proteins">
556 <input type="hidden" name="CMD" value="Put"></td></tr></table>
557 </form></div>
558 <div id="blastndescription" class="description">
559 <table border="0" cellpadding="0" cellspacing="0" width="204">
560 <tr>
561 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>BLASTN</b></td>
562 <td align="right"><a href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
563 </tr>
564 <tr><td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td></tr><tr><td colspan="2" class="size1">Search a nucleotide sequence against GenBank on NCBI server. <b>Query type:</b> DNA sequence. <b>Required option:</b> None.</td></tr></table>
565 </div><div id="blastn" class="optionlist">
566 <form name="blastnform">
567 <table width="600" border="0" bgcolor="#e6e6e6" cellpadding="5" cellspacing="5">
568 <tr><td class="size1"><p class="size2"><font color="#cc0000"><b>blastn</b></font></p>
569
570 <p><b>Set subsequence: From</b>
571 <input type="text" size="15" name="QUERY_FROM" value="">
572 <b>To</b>
573 <input type="text" size="15" name="QUERY_TO" value="">
574 <p><b>Database</b> <select name="DATABASE">
575 <option selected >nr
576 <option >est
577 <option >est_human
578 <option >est_mouse
579 <option >est_others
580 <option >gss
581 <option >htgs
582 <option >pat
583 <option >yeast
584 <option >mito
585 <option >vector
586 <option >ecoli
587 <option >pdb
588 <option >Drosophila genome
589 <option >month
590 <option >alu
591 <option >dbsts
592 </select>
593 <hr noshade size="1">
594 <b>Limit by Entrez query</b>
595 <input type="text" size="15" name="ENTREZ_QUERY" value=""><b>or select from</b> <select name="ENTREZ_QUERY">
596 <option selected >(none)
597 <option >Viruses [ORGN]
598 <option >Archaea [ORGN]
599 <option >Bacteria [ORGN]
600 <option >Eukaryota [ORGN]
601 <option >Viridiplantae [ORGN]
602 <option >Fungi [ORGN]
603 <option >Metazoa [ORGN]
604 <option >Arthropoda [ORGN]
605 <option >Vertebrata [ORGN]
606 <option >Mammalia [ORGN]
607 <option >Rodentia [ORGN]
608 <option >Primates [ORGN]
609 <option >-------------------
610 <option >Aeropyrum pernix [ORGN]
611 <option >Aquifex aeolicus [ORGN]
612 <option >Arabidopsis thaliana [ORGN]
613 <option >Bacillus subtilis [ORGN]
614 <option >Bos taurus [ORGN]
615 <option >Caenorhabditis elegans [ORGN]
616 <option >Danio rerio [ORGN]
617 <option >Dictyostelium discoideum [ORGN]
618 <option >Drosophila melanogaster [ORGN]
619 <option >Escherichia coli [ORGN]
620 <option >Gallus gallus [ORGN]
621 <option >Homo sapiens [ORGN]
622 <option >Human immunodeficiency virus type 1 [ORGN]
623 <option >Methanococcus jannaschii [ORGN]
624 <option >Mus musculus [ORGN]
625 <option >Oryctolagus cuniculus [ORGN]
626 <option >Oryza sativa [ORGN]
627 <option >Ovis aries [ORGN]
628 <option >Plasmodium falciparum [ORGN]
629 <option >Rattus norvegicus [ORGN]
630 <option >Saccharomyces cerevisiae [ORGN]
631 <option >Schizosaccharomyces pombe [ORGN]
632 <option >Simian immunodeficiency virus [ORGN]
633 <option >Synechocystis PCC6803 [ORGN]
634 <option >Takifugu rubripes [ORGN]
635 <option >Xenopus laevis [ORGN]
636 <option >Zea mays [ORGN]
637 </select><p>
638 <b>Choose filter:</b>
639 <input type="checkbox" name="FILTER" value="L" checked>
640 <b>Low complexity</b>
641 <input type="checkbox" name="FILTER" value="R">
642 <b>Human repeats</b>
643 <input type="checkbox" name="FILTER" value="m">
644 <b>Mask for lookup table only</b>
645 <input type="checkbox" name="LCASE_MASK" value="on">
646 <b>Mask lower case</b>
647 <p><b>Expect</b>
648 <input type="text" size="15" name="EXPECT" value="10"><b>Word size</b> <select name="WORD_SIZE">
649 <option >7
650 <option selected >11
651 <option >15
652 </select>
653 <p><b>Other advanced option</b>
654 <input type="text" size="15" name="OTHER_ADVANCED" value=""><p>
655 <hr noshade size="1">
656 <b>Show:</b>
657 <input type="checkbox" name="SHOW_OVERVIEW" value="on" checked>
658 <b>graphical overview</b>
659 <input type="checkbox" name="NCBI_GI" value="on" checked>
660 <b>NCBI-GI</b><select name="FORMAT_OBJECT">
661 <option selected value="Alignment">Alignment
662 <option value="PSSM">PSSM
663 <option value="Bioseq">Bioseq
664 </select><p><b>Format type</b> <select name="FORMAT_TYPE">
665 <option selected value="HTML">HTML
666 <option value="Text">Plain text
667 <option value="ASN.1">ASN.1
668 <option value="XML">XML
669 </select><p><b>Number of descriptions</b> <select name="DESCRIPTIONS">
670 <option >0
671 <option >10
672 <option >50
673 <option selected >100
674 <option >250
675 <option >500
676 <option >1000
677 </select><p><b>Number of alignments</b> <select name="ALIGNMENTS">
678 <option >0
679 <option >10
680 <option selected >50
681 <option >100
682 <option >250
683 <option >500
684 <option >1000
685 </select><p><b>Alignment view</b> <select name="ALIGNMENT_VIEW">
686 <option selected value="Pairwise">Pairwise
687 <option value="QueryAnchored">query-anchored with identities
688 <option value="QueryAnchoredNoIdentities">query-anchored without identities
689 <option value="FlatQueryAnchored">flat query-anchored with identities
690 <option value="FlatQueryAnchoredNoIdentities">flat query-anchored without identities
691 </select><p><b>Layout</b> <select name="LAYOUT">
692 <option value="OneWindow">One Window
693 <option selected value="TwoWindows">Two Windows
694 </select><p><b>Formatting options on page with results</b> <select name="FORMAT_BLOCK_ON_RESPAGE">
695 <option selected value="None">None
696 <option value="Top">At the top
697 <option value="Bottom">At the bottom
698 </select><p><b>Autoformat</b> <select name="AUTO_FORMAT">
699 <option value="Off">Off
700 <option selected value="Semiauto">Semi-auto
701 <option value="Fullauto">Full-auto
702 </select>
703 <p><b>Send results by e-mail</b>
704 <input type="text" size="15" name="EMAIL_ADDRESS" value="">
705 <input type="hidden" name="PROGRAM" value="blastn">
706 <input type="hidden" name="CLIENT" value="web">
707 <input type="hidden" name="SERVICE" value="plain">
708 <input type="hidden" name="PAGE" value="Nucleotides">
709 <input type="hidden" name="CMD" value="Put"></td></tr></table>
710 </form></div>
711 <div id="translate_blastdescription" class="description">
712 <table border="0" cellpadding="0" cellspacing="0" width="204">
713 <tr>
714 <td class="size2"><img height="8" width="8" src="images/redear.png"><b>Translated BLAST</b></td>
715 <td align="right"><a href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=1&HITLIST_SIZE=100&NCBI_GI=on&PAGE=Translations&PROGRAM=blastx&SERVICE=plain&SET_DEFAULTS.x=37&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=no&END_OF_HTTPGET=Yes" target="_blank"><img border="0" height="12" width="32" src="images/more_grey.png"></a></td>
716 </tr>
717 <tr><td height="1" colspan="2" bgcolor="#cccccc"><spacer type="block" width="32" height="1"></td></tr><tr><td colspan="2" class="size1">Translated BLAST are a set of BLAST programs that first translate your DNA sequence and searches database of protein sequence/ translated nucleotide sequence. <b>Default program BLASTX.</b><b>Query type: DNA sequence. Required option: none.</b></td></tr></table>
718 </div><div id="translate_blast" class="optionlist">
719 <form name="translate_blastform">
720 <table width="600" border="0" bgcolor="#e6e6e6" cellpadding="5" cellspacing="5">
721 <tr><td class="size1"><p class="size2"><font color="#cc0000"><b>Translated BLAST</b></font></p>
722
723 <input type="hidden" name="UNGAPPED_ALIGNMENT" value="no"><p><b>Choose program</b> <select name="PROGRAM">
724 <option selected value="blastx">TRANSLATED query - PROTEIN database [blastx]
725 <option value="tblastn">PROTEIN query - TRANSLATED database [tblastn]
726 <option value="tblastx">TRANSLATED query - TRANSLATED database [tblastx]
727 </select>
728 <p><b>Set subsequence: From</b>
729 <input type="text" size="15" name="QUERY_FROM" value="">
730 <b>To</b>
731 <input type="text" size="15" name="QUERY_TO" value=""><p><b>Choose database</b> <select name="DATABASE">
732 <option selected >nr
733 <option >swissprot
734 <option >prat
735 <option >yeast
736 <option >ecoli
737 <option >pdb
738 <option >Drosophila genome
739 <option >month
740 </select><p><b>Genetic code</b> <select name="GENETIC_CODE">
741 <option selected >Standard (1)
742 <option >Vertebrate Mitochondrial (2)
743 <option >Yeast Mitochondrial (3)
744 <option >Mold Mitochondrial; ... (4)
745 <option >Invertebrate Mitochondrial (5)
746 <option >Ciliate Nuclear; ... (6)
747 <option >Echinoderm Mitochondrial (9)
748 <option >Euplotid Nuclear (10)
749 <option >Bacterial (11)
750 <option >Alternative Yeast Nuclear (12)
751 <option >Ascidian Mitochondrial (13)
752 <option >Flatworm Mitochondrial (14)
753 <option >Blepharisma Macronuclear (15)
754 </select>
755 <hr noshade size="1">
756 <b>Limit by Entrez query</b>
757 <input type="text" size="15" name="ENTREZ_QUERY" value=""><b>or select from</b> <select name="ENTREZ_QUERY">
758 <option selected >(none)
759 <option >Viruses [ORGN]
760 <option >Archaea [ORGN]
761 <option >Bacteria [ORGN]
762 <option >Eukaryota [ORGN]
763 <option >Viridiplantae [ORGN]
764 <option >Fungi [ORGN]
765 <option >Metazoa [ORGN]
766 <option >Arthropoda [ORGN]
767 <option >Vertebrata [ORGN]
768 <option >Mammalia [ORGN]
769 <option >Rodentia [ORGN]
770 <option >Primates [ORGN]
771 <option >-------------------
772 <option >Aeropyrum pernix [ORGN]
773 <option >Aquifex aeolicus [ORGN]
774 <option >Arabidopsis thaliana [ORGN]
775 <option >Bacillus subtilis [ORGN]
776 <option >Bos taurus [ORGN]
777 <option >Caenorhabditis elegans [ORGN]
778 <option >Danio rerio [ORGN]
779 <option >Dictyostelium discoideum [ORGN]
780 <option >Drosophila melanogaster [ORGN]
781 <option >Escherichia coli [ORGN]
782 <option >Gallus gallus [ORGN]
783 <option >Homo sapiens [ORGN]
784 <option >Human immunodeficiency virus type 1 [ORGN]
785 <option >Methanococcus jannaschii [ORGN]
786 <option >Mus musculus [ORGN]
787 <option >Oryctolagus cuniculus [ORGN]
788 <option >Oryza sativa [ORGN]
789 <option >Ovis aries [ORGN]
790 <option >Plasmodium falciparum [ORGN]
791 <option >Rattus norvegicus [ORGN]
792 <option >Saccharomyces cerevisiae [ORGN]
793 <option >Schizosaccharomyces pombe [ORGN]
794 <option >Simian immunodeficiency virus [ORGN]
795 <option >Synechocystis PCC6803 [ORGN]
796 <option >Takifugu rubripes [ORGN]
797 <option >Xenopus laevis [ORGN]
798 <option >Zea mays [ORGN]
799 </select><p>
800 <b>Choose filter</b>
801 <input type="checkbox" name="FILTER" value="L" checked>
802 <b>Low complexity</b>
803 <input type="checkbox" name="FILTER" value="m">
804 <b>Mask for lookup table only</b>
805 <input type="checkbox" name="LCASE_MASK" value="on">
806 <b>Mask lower case</b>
807 <p><b>Expect</b>
808 <input type="text" size="15" name="EXPECT" value="10"><p><b>Word Size</b> <select name="WORD_SIZE">
809 <option >2
810 <option selected >3
811 </select><p><b>Matrix</b> <select name="MATRIX_NAME">
812 <option >PAM30
813 <option >PAM70
814 <option >BLOSUM80
815 <option selected >BLOSUM62
816 <option >BLOSUM45
817 </select><p><b>Gap cost</b> <select name="GAPCOSTS">
818 <option selected >11 1
819 <option >9 2
820 <option >8 2
821 <option >7 2
822 <option >12 1
823 <option >10 1
824 </select>
825 <p><b>Other advanced option</b>
826 <input type="text" size="15" name="OTHER_ADVANCED" value=""><p>
827 <hr noshade size="1">
828 <b>Show:</b>
829 <input type="checkbox" name="SHOW_OVERVIEW" value="on" checked>
830 <b>overview</b>
831 <input type="checkbox" name="NCBI_GI" value="on" checked>
832 <b>NCBI-GI</b><select name="FORMAT_OBJECT">
833 <option selected value="Alignment">Alignment
834 <option value="PSSM">PSSM
835 <option value="Bioseq">Bioseq
836 </select><p><b>Format</b> <select name="FORMAT_TYPE">
837 <option selected value="HTML">HTML
838 <option value="Text">Plain text
839 <option value="ASN.1">ASN.1
840 <option value="XML">XML
841 </select><p><b>Number of descriptions</b> <select name="DESCRIPTIONS">
842 <option >0
843 <option >10
844 <option >50
845 <option selected >100
846 <option >250
847 <option >500
848 <option >1000
849 </select><p><b>Number of alignments</b> <select name="ALIGNMENTS">
850 <option >0
851 <option >10
852 <option selected >50
853 <option >100
854 <option >250
855 <option >500
856 <option >1000
857 </select><p><b>Alignment view</b> <select name="ALIGNMENT_VIEW">
858 <option selected value="Pairwise">Pairwise
859 <option value="QueryAnchored">query-anchored with identities
860 <option value="QueryAnchoredNoIdentities">query-anchored without identities
861 <option value="FlatQueryAnchored">flat query-anchored with identities
862 <option value="FlatQueryAnchoredNoIdentities">flat query-anchored without identities
863 <option value="Tabular">Hit Table
864 </select><p><b>Layout</b> <select name="LAYOUT">
865 <option value="OneWindow">One Window
866 <option selected value="TwoWindows">Two Windows
867 </select><p><b>Formatting options on page with results</b> <select name="FORMAT_BLOCK_ON_RESPAGE">
868 <option selected value="None">None
869 <option value="Top">At the top
870 <option value="Bottom">At the bottom
871 </select><p><b>Autoformat</b> <select name="AUTO_FORMAT">
872 <option value="Off">Off
873 <option selected value="Semiauto">Semi-auto
874 <option value="Fullauto">Full-auto
875 </select>
876 <p><b>Send results by e-mail</b>
877 <input type="text" size="15" name="EMAIL_ADDRESS" value="">
878 <input type="hidden" name="CLIENT" value="web">
879 <input type="hidden" name="SERVICE" value="plain">
880 <input type="hidden" name="PAGE" value="Translations">
881 <input type="hidden" name="CMD" value="Put"></td></tr></table>
882 </form></div>
883 <!--Section #4 and #5 goes here-->
884
885
886
887 </body>
888
889 </html>