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Add sequence search help.

<h1>Searching for Sequences or Patterns</h1>

<p>In order to find a match for a DNA or protein sequence, you will
first need to determine which data to search against. You may pick an
individual NMPDR or supporting genome to match to from the "Pick an
NMPDR Genome" and "Pick a Supporting Genome" dropdowns. If you wish to
search against the entire set of NMPDR or supporting genomes, choose
"All NMPDR Genomes" or "All Supporting Genomes" from the dropdown.
<p>
Next you will choose the desired tool from the "Choose a tool" dropdown.
We support the five standard 
<a href="http://www.ba.itb.cnr.it/BIG/Blast/docs/blast_help.html">BLAST
algorithms</a>. Two act upon a protein query sequence:
<p>
<table>
<tr valign="top"><td> <b>blastp</b></td><td>    compares an amino acid query  sequence  against  a
               protein sequence database;</td></tr>

<tr valign="top"><td>      <b>tblastn </b></td><td>   compares  a  protein  query  sequence  against   a
               nucleotide     sequence    database    dynamically
               translated  in  all  six  reading   frames   (both
               strands).</td></tr>
</table>

<p>while the remaining three act upon a nucleotide query sequence:</p>

<table >

<tr valign="top"><td> <b>blastn </b></td><td>   compares a nucleotide  query  sequence  against  a
               nucleotide sequence database;</td></tr>

<tr valign="top"><td>      <b>blastx  </b></td><td>   compares  the  six-frame  conceptual   translation
               products  of  a  nucleotide  query  sequence (both
               strands) against a protein sequence database;</td></tr>


<tr valign="top"><td>      <b>tblastx  </b></td><td>  compares the six-frame translations of  a
  nucleotide query sequence against the six-frame translations of a nucleotide sequence database.</td></tr>
</table>

<p>
We also support searching for patterns via the scan_for_matches
tool. You may read more about using scan_for_matches
<a href="scan_for_matches.html">here</a>.
<p>
If you know them, you may supply extra command line options to the
tools in the "Options" field.
<p>
Paste the sequence or pattern in the textbox, and press "Search for
Matches". This will run the specified search tool, and present the
output in the web page. If you have chosen a BLAST search against a
particular organism, the results will include the full BLAST output
preceded by a table summarizing the results. If you chose to search
against all organisms, you will only see the summary table.

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