blast/megablast_cs.html
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/* $Id: megablast_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.
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* 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.
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* File Name: $RCSfile: megablast_cs.html,v $
*
* Author: Ilya Dondoshansky
*
* Initial Version Creation Date: 03/14/2000
*
* $Revision: 1.4 $
*
* File Description:
* Template for standalone Mega BLAST Web page
*
* $Log: megablast_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 2003/05/05 18:14:02 dondosha
* Uncommented discontiguous megablast options; added subsequence options
*
* Revision 1.2 2002/08/06 20:09:19 dondosha
* Added commented out HTML code for discontiguous word 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/megablast_form.gif" ISMAP>
<IMG SRC="images/megablast_form.gif" BORDER=0 ISMAP></A>
<HEAD>
<SCRIPT>
function megablastDefaults(f, on, off) {
if (on && !off) {
f.UNGAPPED_ALIGNMENT.checked = off;
}
if (off && (on || f.MEGABLAST.checked)) {
f.MEGABLAST.checked = !off;
}
}
</SCRIPT>
</HEAD>
<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: BLASTN </a>
<INPUT TYPE="checkbox" NAME="MEGABLAST" VALUE="is_set" CHECKED onClick="megablastDefaults(this.form,1,!checked);"> Use <a href="docs/megablast_readme.html">MegaBlast</a>
<P>
<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
<INPUT TYPE="checkbox" NAME="LCASE_MASK"> Mask lower case
<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>
<INPUT TYPE="checkbox" NAME="UNGAPPED_ALIGNMENT" VALUE="is_set" onClick="megablastDefaults(this.form,0, checked);"> Perform ungapped alignment
<P>
<a href="docs/megablast_readme.html">Word Size</a>
<select name="WORD_SIZE">
<option value="11">12</option>
<option value="12">12</option>
<option value="16">16</option>
<option value="20">20</option>
<option value="24">24</option>
<option value="28" selected>28</option>
<option value="32">32</option>
<option value="48">48</option>
<option value="64">64</option>
</select>
<a href="docs/megablast_readme.html" >Percent Identity</a>
<select name="PERC_IDENT">
<option value=0 selected>None</option>
<option>99</option>
<option>98</option>
<option>95</option>
<option>90</option>
<option>85</option>
<option>80</option>
<option>75</option>
<option>70</option>
<option>60</option>
</select>
<P>
<tr>
<td align="right" valign="middle"><a href="docs/discontiguous.html">Discontiguous
Word options</a></font></td>
<td align="left" nowrap valign="CENTER"> <font size="-1">Template length
<select name="TEMPLATE_LENGTH">
<option value=0 selected>Contiguous</option>
<option>16</option>
<option>18</option>
<option>21</option>
</select></font><font size="-1">Template type <select name="TEMPLATE_TYPE" size="0"
><option selected value="0">Coding</option>
<option value="1">Non-coding</option>
<option value="2">Two templates</option>
</select></font><font size="-1">Require 2 word hits for extension <input name="TWO_
HITS" type="checkbox"></font></td>
<P>
<a href="docs/full_options.html">Other advanced options:</a>
<INPUT TYPE="text" NAME="OTHER_ADVANCED" 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> query-anchored with identities
<option value=2> query-anchored without identities
<option value=3> flat query-anchored with identities
<option value=4> flat query-anchored without identities
<option value=7> BLAST XML
<option value=9> 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>
<a href="docs/megablast_readme.html">Return alignment endpoints only</a>
<input name="ENDPOINTS" type="checkbox">
<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 -->
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Last modified: Jan 11, 2002
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</HTML>