From 177afd7397be932b091ea331af70ae582f86c0f3 Mon Sep 17 00:00:00 2001
From: Marco Del Tufo <marco.deltufo@exact-lab.it>
Date: Tue, 4 Jul 2023 14:28:28 +0000
Subject: [PATCH] Update search-domain-services.md

---
 .../search-domain-services.md                          | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md b/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md
index 4ab66ce199b..65cc4342535 100644
--- a/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md
+++ b/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md
@@ -1,12 +1,12 @@
 Search Domain Services
 ======================
 
-|                |ASCII                          |
+|Name            |Description                    |
 |----------------|-------------------------------|
-|`evalue`        |`'Isn't this fun?'`            |
-|Quotes          |`"Isn't this fun?"`            |
-|Dashes          |Defines values for a set of parameters of the tools blastn and blastp. Possible values are<ul><li>blastn: Default value blastn</li></ul><table>  <thead>  <tr>  <th></th>  <th>ASCII</th>  <th>HTML</th>  </tr>  </thead>  <tbody>  <tr>  <td>Single backticks</td>  <td><code>'Isn't this fun?'</code></td>  <td>‘Isn’t this fun?’</td>  </tr>  <tr>  <td>Quotes</td>  <td><code>"Isn't this fun?"</code></td>  <td>“Isn’t this fun?”</td>  </tr>  <tr>  <td>Dashes</td>  <td><code>-- is en-dash, --- is em-dash</code></td>  <td>– is en-dash, — is em-dash</td>  </tr> <tr>  <td>Dashes</td>  <td><code>-- is en-dash, --- is em-dash</code></td>  <td>– is en-dash, — is em-dash</td>  </tr> </tbody>  </table><ul><li>blastp: Default value blastp</li></ul><table>  <thead>  <tr>  <th></th>  <th>ASCII</th>  <th>HTML</th>  </tr>  </thead>  <tbody>  <tr>  <td>Single backticks</td>  <td><code>'Isn't this fun?'</code></td>  <td>‘Isn’t this fun?’</td>  </tr>  <tr>  <td>Quotes</td>  <td><code>"Isn't this fun?"</code></td>  <td>“Isn’t this fun?”</td>  </tr>  <tr>  <td>Dashes</td>  <td><code>-- is en-dash, --- is em-dash</code></td>  <td>– is en-dash, — is em-dash</td>  </tr>  </tbody>  </table>     |
-|Dashes          |`-- is en-dash, --- is em-dash`|
+|`evalue`        |Defines the threshold of so-called "Expect Value" of found matches (for details see http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect and http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf). Higher values means more found matches. Default value is 10.|
+|`word_size`     |Word size for initial match. Decreasing word size results in increasing number of matches. Default values (if `task` parameter hasn't been specified): 11 for `blastn` and 3 for `blastp`.|
+|`task`          |Defines values for a set of parameters of the tools blastn and blastp. Possible values are<ul><li>blastn: Default value blastn</li></ul><table>  <thead>  <tr>  <th>Value</th>  <th>Description</th>  <th>Default value of word_size</th>  </tr>  </thead>  <tbody>  <tr>  <td>blastn-short</td>  <td><code>`blastn` program optimized for sequences shorter than 50 bases</code></td>  <td>7</td>  </tr>  <tr>  <td>blastn</td>  <td><code>Traditional `blastn` requiring an exact match of 11</code></td>  <td>11</td>  </tr>  <tr>  <td>dc-megablast</td>  <td><code>Discontiguous megablast used to find more distant (e.g., interspecies) sequences</code></td>  <td>11</td>  </tr> <tr>  <td>megablast</td>  <td><code>Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</code></td>  <td>28</td>  </tr> </tbody>  </table><ul><li>blastp: Default value blastp</li></ul><table>  <thead>  <tr>  <th></th>  <th>ASCII</th>  <th>HTML</th>  </tr>  </thead>  <tbody>  <tr>  <td>Single backticks</td>  <td><code>'Isn't this fun?'</code></td>  <td>‘Isn’t this fun?’</td>  </tr>  <tr>  <td>Quotes</td>  <td><code>"Isn't this fun?"</code></td>  <td>“Isn’t this fun?”</td>  </tr>  <tr>  <td>Dashes</td>  <td><code>-- is en-dash, --- is em-dash</code></td>  <td>– is en-dash, — is em-dash</td>  </tr>  </tbody>  </table>     |
+|ungapped        |If specified (with an empty string value) only ungapped matches are returned. Will be ignored for `blastp`.|
 
 A search domain service is a DSS plugin which allows to query some
 domain specific search services. For example, a search service on a
-- 
GitLab