GenDBWiki/WebDocumentation/DialogWindows/PatScan

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.

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.