GenDBWiki/WebDocumentation/DialogWindows/PatScan: Difference between revisions
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[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$patscan1.png]] | [[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$patscan1.png]] | ||
The interface consists of 4 categories: | |||
{| border="1" cellpadding="2" cellspacing="0" | |||
| '''Options''' | |||
| Define the type of regions to be searched | |||
|- | |||
| | |||
| Define search strand | |||
|- | |||
| | |||
| Defined the offset which is used to search also characters infront or behind the actual search-region | |||
|- | |||
| '''Search definition''' | |||
| Enter your search pattern here. | |||
|- | |||
| | |||
| Optionally you can check the "use" checkbox to define the insertions/deletions/substitutions if you have not already defined it in your pattern | |||
|- | |||
| | |||
| Above the textfield are two links. "Ambiguity codes" shows you the available IUPAC codes which can be incorporated into your pattern | |||
|- | |||
| | |||
| The second link "Examples" shows you some common example queries for a quick start building your own search patterns | |||
|- | |||
| '''Filter''' | |||
| GenDB tries to associate regions with the PatScan matches. Sometimes you are only interested in matches which are infront | |||
|- | |||
| | |||
| or behind a region,like RBS. So here you can define whether all matches should be displayed, only matches which lie within the bounds of | |||
|- | |||
| | |||
| a region or only intergenic matches. | |||
|- | |||
| '''PatScan''' | |||
| These values should normally not be touched. Only if performance is an issue and you know what you are doing change these values. | |||
|- | |||
| | |||
| Mainly these are commandline options for the scan_for_matches (PatScan) program. For a better description please take a closer look at the [http://www-unix.mcs.anl.gov/compbio/PatScan/HTML/readme_scan_for_matches.html PatScan manual] | |||
|} | |||
A possible main purpose of this tool in GenDB consists of searching for patterns which identify RBS which are located infront of coding regions. | |||
Revision as of 14:21, 23 November 2004
PatScan
PatScan is used to identify patterns in large sequences. It is possible to search patterns by specifying the number of insertions,deltions and substitutions or by defining a weight-matrix.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$patscan1.png
The interface consists of 4 categories:
| Options | Define the type of regions to be searched |
| Define search strand | |
| Defined the offset which is used to search also characters infront or behind the actual search-region | |
| Search definition | Enter your search pattern here. |
| Optionally you can check the "use" checkbox to define the insertions/deletions/substitutions if you have not already defined it in your pattern | |
| Above the textfield are two links. "Ambiguity codes" shows you the available IUPAC codes which can be incorporated into your pattern | |
| The second link "Examples" shows you some common example queries for a quick start building your own search patterns | |
| Filter | GenDB tries to associate regions with the PatScan matches. Sometimes you are only interested in matches which are infront |
| or behind a region,like RBS. So here you can define whether all matches should be displayed, only matches which lie within the bounds of | |
| a region or only intergenic matches. | |
| PatScan | These values should normally not be touched. Only if performance is an issue and you know what you are doing change these values. |
| Mainly these are commandline options for the scan_for_matches (PatScan) program. For a better description please take a closer look at the PatScan manual |
A possible main purpose of this tool in GenDB consists of searching for patterns which identify RBS which are located infront of coding regions.