blast/blast.html
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/* $Id: blast.html,v 1.4 2003/05/22 16:20:45 dondosha Exp $
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* 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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* Please cite the author in any work or product based on this material.
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* File Name: $RCSfile: blast.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.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.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 = "nematostella_vectensis_transcriptome"> nematostella vectensis transcriptome
</select>
<!--
Enter here your input data as
<select name = "INPUT_TYPE">
<option> Sequence in FASTA format
<option> Accession or GI
</select>
-->
<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>
Set subsequence: From
 <input TYPE="text" NAME="QUERY_FROM" VALUE="" SIZE="10">
    To
<input TYPE="text" NAME="QUERY_TO" VALUE="" SIZE="10">
<P>
<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.QUERY_FROM.value='';MainBlastForm.QUERY_TO.value='';MainBlastForm.SEQUENCE.focus();">
<INPUT TYPE="submit" VALUE="Search">
<HR>
The query sequence is
<a href="docs/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>
<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> 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=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>
<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>