PiNAT

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Contents

Intro

PiNAT assesses protein protein interaction (PPI) networks and simulates the flow of processes and pathways in the cell. The input to PiNAT a list of protein identifiers. These identifiers are used to query PPI databases, to retrieve all experimentally known interactions, to build a network,and to render this network on the image of a cell according to the predicted localization of the interactions.

Response times are usually larger than minutes because PiNAT queries require heavy CPU usage.

Reference

Create and assess protein networks through molecular characteristics of individual proteins

Availability

We are currently working on a new release for the pinat software. please forward any questions or comments to assistant at rostlab dot org.

How to use PiNAT

Input:

You can submit a list of protein names (UniProt, Swissprot / Trebml, Genbank or DIP) You can also submit your own network.

Parameters:

You should specify the depth of the PPI network around your query proteins. A depth of 1 means that PiNAT will retrieve all the interactions that involve your query proteins. A depth of 2 will retrieve also the interactions that involve proteins of depth 1, and so forth.Output: PiNat returns two types of output:

  1. a table with the biological reasonabilty of each PPI (Low, Neutral or High), based on two different assessments.
  2. A schematic representation of the process in the cell. It also returns a GML file that could be downloaded and viewed with cytoscape.
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