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

How does the search work

Basically GenDB fetches all regions of the type you specified in the options section and runs PatScan for each region. By default only upstream sequences are searched. But you can override this behaviour by selecting the "both strands" radiobox. The result shows the region marked as big red bars and the PatScan matches are shown as small yellow bars.

Interpretation of Results

The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region. You can see that we specified a offset of 100 bases and filtered all matches which lie within the bounds of a region. As a result we get all intergenic matches which start at maximum 100 bases infront of a region. This can be very handy for identifying RBS regions.