New DNA Sequence Analysis on the NetBeans Platform

ReadXplorer provides straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings.

Above you see the main window with one opened reference and three (two of them are visible) opened track data sets. The mapped reads are classified into three different mapping classes (green - perfect match, yellow - best match, red - common match).

The software extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions.

ReadXplorer is implemented in Java on the NetBeans Platform. Utilizing the NetBeans Platform's modular programming structure, it enables developers to create their own highly specialized software modules and easily plug them into ReadXplorer.

It is created by Rolf Hilker at the University of Giessen.

More info:

http://bioinformatics.oxfordjournals.org/content/early/2014/05/21/bioinformatics.btu205.abstract

http://www.uni-giessen.de/fbz/fb08/bioinformatik/software/ReadXplorer

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About

Geertjan Wielenga (@geertjanw) is a Principal Product Manager in the Oracle Developer Tools group living & working in Amsterdam. He is a Java technology enthusiast, evangelist, trainer, speaker, and writer. He blogs here daily.

The focus of this blog is mostly on NetBeans (a development tool primarily for Java programmers), with an occasional reference to NetBeans, and sometimes diverging to topics relating to NetBeans. And then there are days when NetBeans is mentioned, just for a change.

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