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 4ab66ce199b34a785ad2027519be8e99e67b9abd..65cc43425356a1fd08fdf9e46144d00da887cb6e 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?â€</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?â€</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?â€</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