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<TITLE>SIFT Genome Analysis</TITLE>
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<img src="pics/sifter.gif" align=left width="15%">
<img src="pics/wink-2.jpg" align=right width="10%">
S<font color=red>I</font>F<font color=blue>T</font> Genome 
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<BR><b>SIFT Genome</b>:   Sequences are chosen from NCBI's <A HREF="http://www.ncbi.nlm.nih.gov/sutils/static/blinkhelp.html">precomputed BLAST searches</A>.  Either all BLAST hits can be used in the protein alignment or the top hit to each organism.  Scoring is as described in 
<i>Genome Research </i> <b>12:</b> 436-446.
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This procedure is much faster than having us <A HREF="SIFT_seq_submit2.html">do the search</A>.  You can also <A HREF="SIFT_related_seqs_submit.html">submit your protein sequence
and related sequences</A> or <A HREF="SIFT_aligned_seqs_submit.html">aligned
sequences </A> if you already have them.<BR>


<BR>
<i>Results are deleted after an hour, so please save them! </i>
<BR>
<BR>
[<A HREF="SIFT.html">SIFT home page</A>]
[<A HREF="SIFT_help.html">SIFT help</A>]
</A>
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Enter your email address if you want the results through email : <BR>
<i>Please check that your address is correct and your mailbox is not full.</i><BR>
 <BR>
<INPUT SIZE=50 NAME="address">
</INPUT SIZE>
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<font color=blue>Chromosome Coordinates</font><BR>
One row id, set of chromosome coordinates (begin,end), orientation, nucleotide substitution per line.<BR>
[<A HREF="chr_coords_example.html">Sample format</A>]<BR></font>
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Select Organism (This would be a drop down list)
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<INPUT SIZE=50 NAME="organism">
</INPUT SIZE>
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-and-
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Paste in tab separated list of chromosome coordiantes, orientation (1,-1) and nucleotide substitution <BR>
<TEXTAREA NAME="GI" ROWS=5 COLS=30></TEXTAREA>
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<BR>-or-<BR>
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Upload file containing chromosome cooredinates and nucleotide substitutions<BR>
<INPUT SIZE=50 NAME="GI_file" TYPE="file">
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<INPUT TYPE=submit>
<INPUT TYPE=reset>
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<font color=blue>Parameters</font><BR>
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 Select sequences to include:
  <SELECT NAME="sequences_to_select" SIZE="1">
  <OPTION VALUE="ALL">all BLAST hits 
  <OPTION VALUE="BEST" SELECTED>best BLAST hit to each organism
  </SELECT>
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<i>If you receive a warning that the sequences were not diverse enough for prediction on your substitution, try "all BLAST hits".  If that fails, you can submit <A HREF="
SIFT_seq_submit2.html">here</A> and have SIFT find the appropriate number of sequences.</i><BR>
<BR>
Remove sequences more than
<input type=text name=seq_identity_filter size=3 maxlength = 3 value="90">
percent identical to query<BR>
<i>This cleans out any polymorphic alleles (sequences in the database that
are nearly identical to your
protein but already containing the substitutions of interest).
The contaminating sequences may cause the substitution to be predicted
as tolerated.
</i>
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<BR>
<INPUT TYPE=submit>
<INPUT TYPE=reset>
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<i>Questions or comments?<BR>
Contact <A HREF="/blocks-bin/contact.pl"> us </A><BR>
Last updated:<BR>
November 2008. Bug found where SIFT was not retrieving all the BLAST hits.  Fixed 11/02/2005.<BR>
