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<!DOCTYPE HTML PUBLIC "-//SoftQuad//DTD HoTMetaL PRO 5.0::19980907::extensions to HTML 4.0//EN" "hmpro5.dtd">
<HTML>
<HEAD>
<TITLE>BLAST SNP Sequence</TITLE>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<LINK REL="stylesheet" HREF="NCBI.css">
<SCRIPT LANGUAGE="JavaScript">//<!--
function SetAll( frm, on )
{
for( i = 0; i < 26; i++ ) {
frm.DATABASE[i].checked=on;
}
}
//--></SCRIPT>
</HEAD>
<BODY BGCOLOR="#FFFFFF"
BACKGROUND="/corehtml/bkgd.gif"
TEXT="#000000" VLINK="#CC6600" ALINK="#FF0000">
<IMG SRC="left.gif" ALT="{NCBI LOGO}" WIDTH="130" HEIGHT="45" BORDER="0"
ALIGN="ABSMIDDLE"><IMG SRC="topright.JPG" USEMAP="#top.JPG" BORDER="0"
WIDTH="457" HEIGHT="68" ALIGN="ABSMIDDLE" ALT="dbSNP Logo" HSPACE="10">
<TABLE BORDER="0" WIDTH="600" CELLSPACING="0" CELLPADDING="0">
<!--left column links-->
<TR VALIGN="top">
<TD WIDTH="128"> <IMG SRC="pix_tr.gif" WIDTH="128" HEIGHT="1"><BR> <BR>
<TABLE BORDER="0" WIDTH="128" CELLSPACING="0" CELLPADDING="0">
<TR VALIGN="bottom">
<TD WIDTH="22" CLASS="sidebar-small">&nbsp;</TD>
<TD WIDTH="112" CLASS="sidebar-small"><A
HREF="/SNP"><FONT COLOR="#CCCCFF" SIZE="-1"
FACE="Arial, Helvetica">dbSNP <BR> homepage </FONT></A><BR>
<IMG SRC="pix_tr.gif" WIDTH="1" HEIGHT="2"> </TD>
<TD WIDTH="8" ALIGN="right"><IMG SRC="goup1.gif"
WIDTH="8" HEIGHT="19" ALIGN="RIGHT"><IMG SRC="pix_tr.gif" WIDTH="1" HEIGHT="4">
</TD>
</TR>
<TR ALIGN="right">
<TD COLSPAN="3"><IMG SRC="goup2.gif" WIDTH="128" HEIGHT="12"
ALIGN="RIGHT"><IMG SRC="pix_tr.gif" WIDTH="6" HEIGHT="4"></TD>
</TR>
</TABLE> <BR>
<P CLASS="sidebar"><A HREF="/BLAST/"><FONT
COLOR="#FFCC99" SIZE="-1" FACE="Arial, Helvetica">BLAST Home Page</FONT></A>
</P>
<P CLASS="sidebar-small"><A
HREF="/BLAST/blast_overview.html"><FONT
COLOR="#CCCCFF" SIZE="-1">BLAST overview</FONT></A></P>
<P CLASS="sidebar-small"><A
HREF="/BLAST/blast_FAQs.html"><FONT COLOR="#CCCCFF"
SIZE="-1">BLAST FAQs</FONT></A></P>
<P CLASS="sidebar-small"><A
HREF="/BLAST/blast_whatsnew.html"><FONT
COLOR="#CCCCFF" SIZE="-1">BLAST news</FONT></A></P>
<P CLASS="sidebar-small"><A
HREF="/BLAST/blast_help.html"><FONT COLOR="#CCCCFF"
SIZE="-1">BLAST manual</FONT></A></P>
<!--<P CLASS="sidebar-small"><A HREF="References"><FONT COLOR="#CCCCFF"
SIZE="-1">BLAST references</FONT></A></P>--> </TD>
<TD WIDTH="12"><IMG SRC="pix_tr.gif" WIDTH="12" HEIGHT="1"></TD>
<TD WIDTH="460">
<FORM ACTION="/blast/Blast.cgi" METHOD="post" NAME="listFrm">
<!-- <FORM ACTION="./checkparam.cgi" METHOD="GET" NAME="listFrm">-->
<br>
<P>Select the BLAST program to use and enter your sequence in the
text area below. </P>
<P><A
HREF="/BLAST/blast_program.html">Program</A>
<SELECT NAME="PROGRAM" SIZE="1">
<OPTION SELECTED="SELECTED">blastn</OPTION>
<OPTION>tblastn</OPTION>
</SELECT>
Use Megablast <input type="radio" name ="MEGABLAST" value ="yes" checked> Yes
<input type="radio" name ="MEGABLAST" value ="no"> No
</P>
<TABLE BORDER="0" WIDTH="460" CELLSPACING="2" CELLPADDING="0"
BGCOLOR="#FFFFFF">
<TR>
<TD WIDTH="7" BGCOLOR="#315399">&nbsp;</TD>
<TD WIDTH="303" BGCOLOR="#CCCCFF" CLASS="H3"><FONT
FACE="Arial">&nbsp;Query Sequence</FONT></TD>
</TR>
</TABLE>
<P>Enter your sequence as:
<SELECT NAME="INPUT_TYPE" SIZE="1">
<OPTION>FASTA format</OPTION>
<OPTION SELECTED="SELECTED">Accession or GI</OPTION>
</SELECT> <INPUT TYPE="submit" NAME="submit3"> <BR> <TEXTAREA NAME="QUERY" ROWS="8" COLS="50"></TEXTAREA>
</P>
<!--Top Link Ends -->
<TABLE BORDER="0" WIDTH="460" CELLSPACING="2" CELLPADDING="0"
BGCOLOR="#FFFFFF">
<TR>
<TD WIDTH="7" BGCOLOR="#315399">&nbsp;</TD>
<TD WIDTH="303" BGCOLOR="#CCCCFF" CLASS="H3"><FONT
FACE="Arial">&nbsp;Snp Blast Databases(Human)</FONT></TD>
</TR>
</TABLE>
<TABLE WIDTH="100%">
<TR VALIGN="top">
<TD>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch1.fas" CHECKED="CHECKED"> Chr. 1
<BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch2.fas" CHECKED="CHECKED">
Chr. 2 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch3.fas" CHECKED="CHECKED"> Chr. 3
<BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch4.fas" CHECKED="CHECKED">
Chr. 4 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch5.fas" CHECKED="CHECKED"> Chr. 5
<BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch6.fas" CHECKED="CHECKED">
Chr. 6 <BR> </TD>
<TD>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch7.fas" CHECKED="CHECKED"> Chr. 7
<BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch8.fas" CHECKED="CHECKED">
Chr. 8 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch9.fas" CHECKED="CHECKED"> Chr. 9
<BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch10.fas" CHECKED="CHECKED">
Chr. 10 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch11.fas" CHECKED="CHECKED"> Chr.
11 <BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch12.fas"
CHECKED="CHECKED"> Chr. 12 <BR> </TD>
<TD>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch13.fas" CHECKED="CHECKED"> Chr.
13 <BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch14.fas"
CHECKED="CHECKED"> Chr. 14 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch15.fas" CHECKED="CHECKED"> Chr.
15 <BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch16.fas"
CHECKED="CHECKED"> Chr. 16 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch17.fas" CHECKED="CHECKED"> Chr.
17 <BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch18.fas"
CHECKED="CHECKED"> Chr. 18 <BR> </TD>
<TD>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch19.fas" CHECKED="CHECKED"> Chr.
19 <BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch20.fas"
CHECKED="CHECKED"> Chr. 20 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch21.fas" CHECKED="CHECKED"> Chr.
21 <BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_ch22.fas"
CHECKED="CHECKED"> Chr. 22 <BR>
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_chX.fas" CHECKED="CHECKED"> Chr. X
<BR> <INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_chY.fas" CHECKED="CHECKED">
Chr. Y <BR> </TD>
</TR>
<TR VALIGN="top">
<TD COLSPAN="1">
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_chMulti.fas" CHECKED="CHECKED"> MultiChr. </TD>
<TD COLSPAN="1">
<INPUT TYPE="checkbox" NAME="DATABASE" VALUE="rs_chNotOn.fas" CHECKED="CHECKED"> NotOnChr. </TD>
<TD COLSPAN="2">
<INPUT TYPE="checkbox" NAME="checkbox"
VALUE="ch1 ch2 ch3 ch4 ch5 ch6 ch7 ch8 ch9 ch10 ch11 ch12 ch13 ch14 ch15 ch16 ch17 ch18 ch19 ch20 ch21 ch22 chMulti chNotOn chX chY"
ONCLICK="SetAll(this.form,checked);" CHECKED="CHECKED"> <B>All of the Above
</B></TD>
</TR>
</TABLE> <BR>
<!--Bottom Link Starts -->
<TABLE BORDER="0" WIDTH="460" CELLSPACING="2" CELLPADDING="0"
BGCOLOR="#FFFFFF">
<TR>
<TD WIDTH="7" BGCOLOR="#315399">&nbsp;</TD>
<TD WIDTH="303" BGCOLOR="#CCCCFF" CLASS="H3">
<FONT FACE="Arial">&nbsp;BLAST Search Options</FONT>
<INPUT TYPE="hidden" NAME="WWW_BLAST_TYPE" VALUE="SNP">
<!--<INPUT TYPE="hidden" NAME="DATABASE" VALUE="snp">-->
<INPUT TYPE="hidden" NAME="NOENTREZLINKS"> </TD>
<INPUT TYPE="hidden" NAME="DB_DIR_PREFIX" VALUE="snp/human_9606">
<input name="ALIGNMENT_VIEW" type="hidden" value="PairwiseWithIdentities">
<input name="AUTO_FORMAT" type="hidden" value="Semin_auto">
<INPUT TYPE="hidden" NAME="CMD" VALUE="Put">
</TR>
</TABLE>
<TABLE BORDER="0" CELLPADDING="4" STYLE="color: black">
<TR>
<TH><FONT COLOR="#000000"><A
HREF="/BLAST/newoptions.html#expect">Expect</A></FONT>
</TH>
<!--<TH><FONT COLOR="#000000"><A
HREF="/BLAST/newoptions.html#filter">Filter</A></FONT>
</TH>-->
<TH><FONT COLOR="#000000"><A
HREF="/BLAST/newoptions.html#descriptions">Descriptions</A>
</FONT></TH>
<TH><FONT COLOR="#000000"><A
HREF="/BLAST/newoptions.html#alignments">Alignments</A>
</FONT></TH>
</TR>
<TR>
<TD>
<SELECT NAME="EXPECT" SIZE="1">
<OPTION>0.0001</OPTION>
<OPTION>0.001 </OPTION>
<OPTION SELECTED="SELECTED">0.01</OPTION>
<OPTION>1</OPTION>
<OPTION>10</OPTION>
</SELECT> </TD>
<!--<TD> <SELECT NAME="FILTER" SIZE="1"> <OPTION>default</OPTION> <OPTION>none
</OPTION> </SELECT>
</TD>-->
<TD>
<SELECT NAME="DESCRIPTIONS" SIZE="1">
<OPTION>0</OPTION>
<OPTION>10 </OPTION>
<OPTION>50</OPTION>
<OPTION SELECTED="SELECTED">100</OPTION>
<OPTION>250</OPTION>
<OPTION>500</OPTION>
</SELECT> </TD>
<TD>
<SELECT NAME="ALIGNMENTS" SIZE="1">
<OPTION>0</OPTION>
<OPTION>10</OPTION>
<OPTION>50</OPTION>
<OPTION SELECTED="SELECTED">100</OPTION>
<OPTION>250 </OPTION>
<OPTION>500</OPTION>
</SELECT> </TD>
</TR>
</TABLE>
<P><A
HREF="/BLAST/newoptions.html#filter">Filter</A>
<INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED="CHECKED"> Low
complexity <INPUT TYPE="checkbox" VALUE="R" NAME="FILTER"> Human repeats
<INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only <BR>
</P>
<P><A HREF="/BLAST/full_options.html">Other
advanced options:</A>
<INPUT TYPE="text" NAME="OTHER_ADVANCED" MAXLENGTH="50" SIZE="20"> <BR> <BR>
</P>
<!-- <TABLE BORDER="0" WIDTH="460" CELLSPACING="2" CELLPADDING="0"
BGCOLOR="#FFFFFF">
<TR>
<TD WIDTH="7" BGCOLOR="#315399">&nbsp;</TD>
<TD WIDTH="303" BGCOLOR="#CCCCFF" CLASS="H3"><FONT
FACE="Arial">&nbsp;Results by Mail</FONT></TD>
</TR>
</TABLE>
<P>The BLAST server may be very busy during the weekday, resulting in
delays for users. The email option allows a user to receive the results quickly
in a convenient form. If the HTML option is used, the results should be loaded
into a web browser for viewing. </P>
<P> <INPUT TYPE="checkbox" NAME="EMAIL" VALUE="IS_SET"> Send reply to the
Email address: <INPUT TYPE="text" NAME="PATH" MAXLENGTH="50" SIZE="20"></P>
<P> <INPUT TYPE="checkbox" NAME="HTML" VALUE="IS_SET"> In HTML format </P> -->
<P> <INPUT TYPE="submit" NAME="submit2">
<INPUT TYPE="reset" VALUE="Clear Input" NAME="reset"> </P> </FORM> </TD>
</TR>
<TR VALIGN="top">
<TD WIDTH="128">&nbsp;</TD>
<TD WIDTH="12"><IMG SRC="pix_tr.gif" WIDTH="12" HEIGHT="1"></TD>
<TD WIDTH="460">
<P>&nbsp;</P>
<P ALIGN="center"><B>Questions or Comments?<BR> Write to the
<A HREF="mailto:info@ncbi.nlm.nih.gov">NCBI Service Desk</A></B><BR> </P> </TD>
</TR>
</TABLE>
<P>&nbsp;</P>
<P>&nbsp;</P>
<P>&nbsp;</P>
<P>&nbsp;</P> </BODY>
</HTML>
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