blast/wblast2_cs.html
<!--
/* $Id: wblast2_cs.html,v 1.1 2002/08/06 19:03:53 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: wblast2_cs.html,v $
*
* Initial Version Creation Date: 11/02/2000
*
* $Revision: 1.1 $
*
* Authors: Ilya Dondoshansky, Sergey Shavirin
*
* File Description:
* Template for standalone BLAST 2 sequences Web page
*
* $Log: wblast2_cs.html,v $
* Revision 1.1 2002/08/06 19:03:53 dondosha
* WWW BLAST server, initial CVS revision
*
-->
<HTML>
<HEAD>
<title>Blast 2 Sequences</title>
<SCRIPT LANGUAGE="Javascript">
<!-- HIDE
function chan(a)
{
alert(a);
if (a.value == 'off') {
document.bl2.gopen.value=11;
document.bl2.gext.value=1;
document.bl2.match.value="";
document.bl2.msmatch.value="";
a.value = 'on';
} else {
document.bl2.gopen.value=5;
document.bl2.gext.value=2;
document.bl2.match.value="1";
document.bl2.msmatch.value="-2";
a.value = 'off';
}
}
function chan_prog(a)
{
if (a.selectedIndex == 0) {
document.bl2.gopen.value = 5;
document.bl2.gext.value = 2;
document.bl2.match.value="1";
document.bl2.msmatch.value="-2";
document.bl2.word.value="11";
document.bl2.matrix.options.length = 1;
document.bl2.matrix.options[0].text='Not Applicable';
} else if (a.selectedIndex >= 1) {
document.bl2.matrix.options.length = 6;
document.bl2.matrix.options[0].text='BLOSUM62';
document.bl2.matrix.options[1].text='PAM30';
document.bl2.matrix.options[2].text='PAM70';
document.bl2.matrix.options[3].text='PAM250';
document.bl2.matrix.options[4].text='BLOSUM90';
document.bl2.matrix.options[5].text='BLOSUM50';
document.bl2.word.value="3";
if (document.bl2.matrix.selectedIndex == 0) {
document.bl2.gopen.value = 11;
document.bl2.gext.value = 1;
} else if (document.bl2.matrix.selectedIndex == 1) {
document.bl2.gopen.value = 9;
document.bl2.gext.value = 1;
} else if (document.bl2.matrix.selectedIndex == 2) {
document.bl2.gopen.value = 10;
document.bl2.gext.value = 1;
} else if (document.bl2.matrix.selectedIndex == 3) {
document.bl2.gopen.value = 14;
document.bl2.gext.value = 2;
} else if (document.bl2.matrix.selectedIndex == 4) {
document.bl2.gopen.value = 10;
document.bl2.gext.value = 1;
} else if (document.bl2.matrix.selectedIndex == 5) {
document.bl2.gopen.value = 13;
document.bl2.gext.value = 2;
}
document.bl2.match.value="";
document.bl2.msmatch.value="";
}
}
function update_mtrx(a)
{
if (document.bl2.program.selectedIndex == 0) {
return;
}
document.bl2.word.value = 3;
if (a.selectedIndex == 0) { /* BLOSUM62 */
document.bl2.gopen.value = 11;
document.bl2.gext.value = 1;
} else if (a.selectedIndex == 1) { /* PAM30 */
document.bl2.gopen.value = 9;
document.bl2.gext.value = 1;
} else if (a.selectedIndex == 2) { /* PAM70 */
document.bl2.gopen.value = 10;
document.bl2.gext.value = 1;
} else if (a.selectedIndex == 3) { /* PAM250 */
document.bl2.gopen.value = 14;
document.bl2.gext.value = 2;
} else if (a.selectedIndex == 4) { /* BLOSUM90 */
document.bl2.gopen.value = 10;
document.bl2.gext.value = 1;
} else if (a.selectedIndex == 5) { /* BLOSUM50 */
document.bl2.gopen.value = 13;
document.bl2.gext.value = 2;
}
}
function clear_sequence() {
document.bl2.seqfile1.value='';
document.bl2.seqfile2.value='';
document.bl2.sseq.value='';
document.bl2.seq.value='';
document.bl2.one.value='';
document.bl2.two.value='';
document.bl2.to.value='';
document.bl2.tto.value='';
document.bl2.from.value='';
document.bl2.ffrom.value='';
document.bl2.seq.focus();
}
// -->
</SCRIPT>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<A HREF="blast_form.map">
<IMG SRC="images/bl2seq.gif" BORDER=0 ISMAP></A>
<FORM NAME="bl2" method="Post" action="wblast2_cs.cgi" enctype="multipart/form-data">
This tool produces the alignment of two given sequences using BLAST<BR>
engine for local alignment.
<P>
<A HREF=docs/blast_program.html>Program</A>
<select name="program" onChange="chan_prog(this)">
<option selected> blastn
<option> blastp
<option> tblastn
<option> blastx
<option> tblastx
</select>
<INPUT TYPE="submit" VALUE="Align">
<INPUT TYPE="button" VALUE="Clear sequence" onClick="clear_sequence()">
<HR>
<font color=ff0000>Sequence 1: </font>
from: <INPUT type=text size=8 name="from"> to:
<INPUT type=text size=8 name="to">
<BR>
Enter accession or GI <INPUT type=text size=8 name="one">
or sequence in FASTA format
<BR>
<textarea name="seq" rows=6 cols=60></textarea><BR>
or download from file <INPUT type=file name="seqfile1">
<P>
<HR>
<font color=ff0000>Sequence 2: </font>
from:<INPUT type=text size=8 name="ffrom"> to:
<INPUT type=text size=8 name="tto">
<BR>
Enter accession or GI <INPUT type=text size=8 name="two">
or sequence in FASTA format
<BR>
<textarea name="sseq" rows=6 cols=60></textarea>
<BR>
or download from file <INPUT type=file name="seqfile2">
<HR>
Parameters used in <A HREF=docs/full_options.html#blastn>BLASTN </A>program only:<BR>
<strong>Reward for a match:</strong><INPUT type=text size=8 name="match" value=1>
<strong>Penalty for a mismatch:</strong><INPUT type=text size=8 name="msmatch" value=-2>
<HR>
<A HREF=docs/options.html#matrix>Matrix</A>
<select name="matrix" onChange="update_mtrx(this)">
<option> Not Applicable
<!-- <option> 0 BLOSUM62
<option> 1 PAM30
<option> 2 PAM70
<option> 3 PAM250
<option> 4 BLOSUM90
<option> 5 BLOSUM50
// -->
</select>
Open gap
<INPUT type=text size=4 name="gopen" value=5>
and extension gap
<INPUT type=text size=4 name="gext" value=2> penalties
<BR>
Gap x_dropoff <INPUT type=text size=4 name="dropoff" value=50>
<A HREF=docs/newoptions.html#expect>Expect value</A>
<INPUT type=text size=4 name="expect" value=10>
Word size <INPUT type=text size=4 name="word" value=11>
<a href="docs/newoptions.html#filter">Filter</a>
<INPUT TYPE="checkbox" NAME="Filter" VALUE="1" CHECKED>
<HR>
<INPUT TYPE="submit" VALUE="Align">
<INPUT TYPE="button" VALUE="Clear sequence" onClick="clear_sequence()">
<INPUT TYPE="reset" VALUE="Reset form">
</form>
<HR>
<ADDRESS> Comments and suggetstions to:
<A HREF="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</A>
<BR>
</body>
</html>