tripal_blast/theme/blast_protein_user_menupage.tpl.php

<?php

/**
 * @file
 *
 */

//eksc- better to get this from module settings
$nucl_blastpath = './blast/nucleotide/nucleotide';
$prot_blastpath = './blast/nucleotide/protein';
?>

<style>
  tr.blast-highlighted td {
    background: #F6FFEC;
  }
</style>

<p>In bioinformatics, BLAST (Basic Local Alignment Search Tool) is an algorithm
for comparing primary biological sequence information, such as the amino-acid
sequences of different proteins or the nucleotides of DNA sequences. A BLAST
search enables a researcher to compare a query sequence with a library or
database of sequences, and identify library sequences that resemble the query
sequence above a certain threshold. Different types of BLASTs are available
according to the query sequences. For example, following the discovery of a
previously unknown gene in the mouse, a scientist will typically perform a
BLAST search of the human genome to see if humans carry a similar gene;
BLAST will identify sequences in the human genome that resemble the mouse
gene based on similarity of sequence.</p>

<blockquote>Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic
local alignment search tool. J. Mol. Biol., 215, 403–410.</blockquote>

<table>
  <tr>
    <th>Query Type</th>
    <th>Database Type</th>
    <th>BLAST Program</th>
  </tr>
  <tr>
    <td rowspan="2">Nucleotide</td>
    <td>Nucleotide</td>
    <td><?php print l('blastn', $nucl_blastpath);?>:
      Search a nucleotide database using a nucleotide query.</td>
  </tr>
  <tr>
    <td>Protein</td>
    <td><?php print l('blastx', $nucl_blastpath);?>:
      Search protein database using a translated nucleotide query.</td>
  </tr>
  <tr class="blast-highlighted">
    <td  rowspan="2">Protein</td>
    <td>Nucleotide</td>
    <td><?php print l('tblastn', $prot_blastpath);?>:
      Search translated nucleotide database using a protein query.</td>
  </tr>
  <tr class="blast-highlighted">
    <td>Protein</td>
    <td><?php print l('blastp', $prot_blastpath);?>:
      Search protein database using a protein query.</td>
  </tr>
</table>