PATTINPROT help

A brief introduction to PATTINPROT
PATTINPROT is a tool to scan a protein database of one or several sequences for one or several patterns. The pattern must be written with the PROSITE syntax. PATTINPROT allows errors towards pattern to find. Errors are set by number of mistmatch allowed or by a similarity threshold towards the pattern.
Algorithm :
In the the algorithm used by PATTINPROT and PROSCAN, the biological information is variably distributed between the pattern elements. To do that, when an element is not respected, it's penalized by its frequency. When a strict element (e.g. -F- ) is not respected, it's a heavy penalty cost for the search. So, the signal-noise ratio is improved.
This algorithm was developped in our laboratory and is included (NPS@ is the original server for it).

Availability in NPS@
PATTINPROT is available :

So, for example, you can use PATTINPROT to filter a database built from an ACNUC query or after a BLAST search.

Parameters
By default the scan is made with no error.
You can set the number of residues to show on both sides of the hit.

NPS@ PATTINPROT output example
The NPS@ PATTINPROT output is divided into three parts.

References


User : public@3.81.28.94. Last modification time : Thu Jan 14 18:31:23 2016. Current time : Sun Aug 25 10:05:05 2019