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idotter

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# iDotter - an interactive dot plot viewer

## Introduction
In bioinformatics, one frequent task is judging the likelihood of
the overall RNA secondary structure. This judgment is based on
comparing the base pair probabilities of RNA secondary structures.
Therefore, the probabilities for two nucleotides of an RNA sequence
forming such base pairs are calculated. Dot plots are used for dis-
playing probabilities or similarity measures between a row and a
column of a matrix. Hence, dot plots are frequently used for RNA
secondary analysis displaying the probability of a row and a column
nucleotide forming a base pair. However, most tools produce only
static dot plot images which restricts possible interactions to the
capabilities of the respective viewers (mostly ps-viewers). Moreover,
this approach does not scale well. Therefore, we developed iDotter,
an interactive tool for analyzing RNA secondary structures. iDotter
overcomes the previously described limitations providing multiple
interaction mechanisms facilitating the interactive analysis of the
displayed data. Our tool proved superior to all previous approaches
and is already regularly used by biologists and bioinformaticians.

## Install 
Clone the project
Install a webserver of your choice (apache, nginx, lighttpd, LAMP, etc)
Install PHP5
Make the git repositority accessible for the webserver

## Usage
Navigate in a webbrowser to localhost/index.php
Upload one of the example postscript files