1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
|
<!--
/* $Id: blast_cs.html,v 1.4 2003/05/22 16:20:45 dondosha Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: $RCSfile: blast_cs.html,v $
*
* Author: Sergei Shavirin
*
* Initial Version Creation Date: 03/14/2000
*
* $Revision: 1.4 $
*
* File Description:
* Template for standalone BLAST Web page
*
* $Log: blast_cs.html,v $
* Revision 1.4 2003/05/22 16:20:45 dondosha
* Removed references to blast_form.map: describe the map inside HTML
*
* Revision 1.3 2003/05/09 17:54:38 dondosha
* Added select menu for database genetic codes
*
* Revision 1.2 2003/05/05 18:14:02 dondosha
* Uncommented discontiguous megablast options; added subsequence options
*
* Revision 1.1 2002/08/06 19:03:51 dondosha
* WWW BLAST server, initial CVS revision
*
-->
<HTML>
<TITLE>BLAST Search </TITLE>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<map name=img_map>
<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
<area shape=rect coords=385,1,435,21 href="index.html">
<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
</map>
<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/blast_form.gif" ISMAP>
<FORM ACTION="blast_cs.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
<B>Choose program to use and database to search:</B>
<P>
<a href="docs/blast_program.html">Program</a>
<select name = "PROGRAM">
<option> blastn
<option> blastp
<option> blastx
<option> tblastn
<option> tblastx
</select>
<a href="docs/blast_databases.html">Database</a>
<select name = "DATALIB">
<option VALUE = "test_na_db"> test_na_db
<option VALUE = "test_aa_db"> test_aa_db
</select>
<P>
Enter here your input data as
<select name = "INPUT_TYPE">
<option> Sequence in FASTA format
<option> Accession or GI
</select>
<INPUT TYPE="submit" VALUE="Search">
<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.QUERY_FROM.value='';MainBlastForm.QUERY_TO.value='';MainBlastForm.SEQUENCE.focus();">
<BR>
<textarea name="SEQUENCE" rows=6 cols=60>
</textarea>
<BR>
Or load it from disk
<INPUT TYPE="file" NAME="SEQFILE">
<P>Please read about <a href="/BLAST/fasta.html">FASTA</a> format description
<P>
Set subsequence: From
 <input TYPE="text" NAME="QUERY_FROM" VALUE="" SIZE="10">
    To
<input TYPE="text" NAME="QUERY_TO" VALUE="" SIZE="10">
<P>
<HR>
The query sequence is
<a href="/BLAST/filtered.html">filtered</a>
for low complexity regions by default.
<BR>
<a href="docs/newoptions.html#filter">Filter</a>
<INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED> Low complexity
<INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
<P>
<a href="docs/newoptions.html#expect">Expect</a>
<select name = "EXPECT">
<option> 0.0001
<option> 0.01
<option> 1
<option selected> 10
<option> 100
<option> 1000
</select>
<a href="docs/matrix_info.html">Matrix</a>
<select name = "MAT_PARAM">
<option value = "PAM30 9 1"> PAM30 </option>
<option value = "PAM70 10 1"> PAM70 </option>
<option value = "BLOSUM80 10 1"> BLOSUM80 </option>
<option selected value = "BLOSUM62 11 1"> BLOSUM62 </option>
<option value = "BLOSUM45 14 2"> BLOSUM45 </option>
</select>
<INPUT TYPE="checkbox" NAME="UNGAPPED_ALIGNMENT" VALUE="is_set"> Perform ungapped alignment
<P>
<a href="docs/newoptions.html#gencodes">Query Genetic Codes (blastx only)
</a>
<select name = "GENETIC_CODE">
<option> Standard (1)
<option> Vertebrate Mitochondrial (2)
<option> Yeast Mitochondrial (3)
<option> Mold Mitochondrial; ... (4)
<option> Invertebrate Mitochondrial (5)
<option> Ciliate Nuclear; ... (6)
<option> Echinoderm Mitochondrial (9)
<option> Euplotid Nuclear (10)
<option> Bacterial (11)
<option> Alternative Yeast Nuclear (12)
<option> Ascidian Mitochondrial (13)
<option> Flatworm Mitochondrial (14)
<option> Blepharisma Macronuclear (15)
</select>
<P>
<a href="docs/newoptions.html#gencodes">Database Genetic Codes (tblast[nx] only)
</a>
<select name = "DB_GENETIC_CODE">
<option> Standard (1)
<option> Vertebrate Mitochondrial (2)
<option> Yeast Mitochondrial (3)
<option> Mold Mitochondrial; ... (4)
<option> Invertebrate Mitochondrial (5)
<option> Ciliate Nuclear; ... (6)
<option> Echinoderm Mitochondrial (9)
<option> Euplotid Nuclear (10)
<option> Bacterial (11)
<option> Alternative Yeast Nuclear (12)
<option> Ascidian Mitochondrial (13)
<option> Flatworm Mitochondrial (14)
<option> Blepharisma Macronuclear (15)
</select>
<P>
<a href="docs/oof_notation.html">Frame shift penalty</a> for blastx
<select NAME = "OOF_ALIGN">
<option> 6
<option> 7
<option> 8
<option> 9
<option> 10
<option> 11
<option> 12
<option> 13
<option> 14
<option> 15
<option> 16
<option> 17
<option> 18
<option> 19
<option> 20
<option> 25
<option> 30
<option> 50
<option> 1000
<option selected VALUE = "0"> No OOF
</select>
<P>
Limit search to results of <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html#Writing_Advanced_Search_Statements">Entrez query</a> <INPUT TYPE="text" NAME = "ENTREZ_QUERY" MAXLENGTH="50">
<P>
<a href="docs/full_options.html">Other advanced options:</a>
<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">
<INPUT TYPE="checkbox" NAME="TAX_BLAST"> Show <a href ="docs/taxblasthelp.html">Tax Blast reports</a>
<HR>
<INPUT TYPE="checkbox" NAME="NCBI_GI" >
<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
<INPUT TYPE="checkbox" NAME="OVERVIEW" CHECKED>
<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
<a href="docs/options.html#alignmentviews">Alignment view</a>
<select name = "ALIGNMENT_VIEW">
<option value=0> Pairwise
<option value=1> master-slave with identities
<option value=2> master-slave without identities
<option value=3> flat master-slave with identities
<option value=4> flat master-slave without identities
<option value=7> BLAST XML
<option value=8> Hit Table
</select>
<BR>
<a href="docs/newoptions.html#descriptions">Descriptions</a>
<select name = "DESCRIPTIONS">
<option> 0
<option> 10
<option> 50
<option selected> 100
<option> 250
<option> 500
</select>
<a href="docs/newoptions.html#alignments">Alignments</a>
<select name = "ALIGNMENTS">
<option> 0
<option> 10
<option selected> 50
<option> 100
<option> 250
<option> 500
</select>
<a href="docs/color_schema.html">Color schema</a>
<select name = "COLOR_SCHEMA">
<option selected value = 0> No color schema
<option value = 1> Color schema 1
<option value = 2> Color schema 2
<option value = 3> Color schema 3
<option value = 4> Color schema 4
<option value = 5> Color schema 5
<option value = 6> Color schema 6
</select>
<P>
<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
<INPUT TYPE="submit" VALUE="Search">
</FORM>
<HR>
<ADDRESS>
Comments and suggestions to:< <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> >
</ADDRESS>
<BR>
<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
<!-- hhmts start -->
Last modified: Jan 11, 2002
<!-- hhmts end -->
</BODY>
</HTML>
|