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=head2 FEATURE COMPARISON

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<table><tr><th>Feature</th><th>Agrep</th><th>GUUGle</th><th>RE</th><th>Vmatch</th></tr><tr><td>Suffix Arrays/Trees</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Sliding Window</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
</tr>
<tr><td>Persistent Index<sup>1</sup></td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Mismatches</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Edit Distance</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Insertions</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
</tr>
<tr><td>Deletions</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
</tr>
<tr><td>Multiple Queries<sup>2</sup></td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>GU</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
</tr>
<tr><td>DNA/RNA</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Protein</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Direct and Revcom</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Reverse Complement</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Upstream/Downstream</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Filters</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Query Length<sup>3</sup></td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
</tr>
<tr><td>Regular Expressions<sup>4</sup></td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
<td style="font-weight: bold;text-align: center;background-color: #00ff00;">yes</td>
<td style="text-align:center;background-color: #ffe0e0;">no</td>
</tr>
</table><br/><div style="font-size: smaller"><hr width="300"
align="left"><sup>1</sup>Needs pre-calculation and (much) more memory but queries are in general faster<br/><sup>2</sup>With query_file<br/><sup>3</sup>Matches if a substring of the query of size n or larger matches<br/><sup>4</sup>Agrep soon</div>

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   Features               || Agrep  | GUUGle |   RE   | Vmatch