blast/psiblast.html
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/* $Id: psiblast.html,v 1.3 2003/06/24 21:53:54 dondosha Exp $
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* 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
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* File Name: $RCSfile: psiblast.html,v $
*
* Author: Sergei Shavirin
*
* Initial Version Creation Date: 03/14/2000
*
* $Revision: 1.3 $
*
* File Description:
* Template for standalone PSI BLAST Web page
*
* $Log: psiblast.html,v $
* Revision 1.3 2003/06/24 21:53:54 dondosha
* Changed WWW_BLAST_TYPE to BLAST_TYPE
*
* Revision 1.2 2003/05/22 16:20:45 dondosha
* Removed references to blast_form.map: describe the map inside HTML
*
* Revision 1.1 2002/08/06 19:03:52 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/psi_blast.gif" ISMAP>
<FORM ACTION="psiblast.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
<INPUT type="hidden" name = "BLAST_TYPE" value = "psiblast">
<B>Choose <a href="docs/blast_databases.html">database</a> to use with PSI/PHI Blast:</B>
<select name = "DATALIB">
<option VALUE = "test_aa_db"> test_aa_db
<option VALUE = "test_na_db"> test_na_db
</select>
<input type="hidden" name = "PROGRAM" value="blastp">
<P>
Enter sequence below in <a href="docs/fasta.html">FASTA</a> format
<BR>
<textarea name="SEQUENCE" rows=6 cols=60>
</textarea>
<BR>
Or load it from disk
<INPUT TYPE="file" NAME="SEQFILE">
<P>
<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQUENCE.focus();">
<INPUT TYPE="submit" VALUE="Search">
<HR>
<a href="docs/newoptions.html#filter">Filter</a>
<INPUT TYPE="checkbox" VALUE="L" NAME="FILTER"> Low complexity
<INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
<P>
<INPUT TYPE="checkbox" NAME="TWEAK_PARAMETERS" CHECKED> <a href ="docs/composition.html">Composition-based statistics</a>
<INPUT TYPE="checkbox" NAME="SMITH_WATERMAN"> Compute Smith-Waterman alignments
<P>
<a href="docs/newoptions.html#alignments">Expect value for inclusion in PSI-BLAST iteration 1</a>
<INPUT TYPE="text" NAME ="E_THRESH" VALUE="0.002" MAXLENGTH="10">
<BR>
<INPUT type="checkbox" NAME="PHI_BLAST">
<a href="docs/pattern.html">Pattern for use in PHI-BLAST search</a>
<INPUT TYPE="text" NAME ="PHI_PATTERN" SIZE="35">
<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>
<P>
<a href="docs/full_options.html">Other advanced options:</a>
<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">
<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> 100
<option> 250
<option selected> 500
</select>
<a href="docs/newoptions.html#alignments">Alignments</a>
<select name = "ALIGNMENTS">
<option> 0
<option> 10
<option> 50
<option> 100
<option> 250
<option selected> 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 -->
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Last modified: Jan 11, 2002
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</BODY>
</HTML>