Open Access Highly Accessed Software

GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures

Björn Hammesfahr1, Florian Odronitz1, Stefanie Mühlhausen1, Stephan Waack2 and Martin Kollmar1*

Author Affiliations

1 Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany

2 Institute of Computer Science, University of Göttingen, Goldschmidtstr. 7, Göttingen, 37077, Germany

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BMC Bioinformatics 2013, 14:77  doi:10.1186/1471-2105-14-77

Published: 4 March 2013

Additional files

Additional file 1:

This file contains the GenePainter software (gene_painter.rb), a README file for installation instructions, the GenePainter documentation, and a script to reconstruct genes via the web service of WebScipio (gene_scan.rb). It also includes example data (MSA, gene and protein structures) used to create the figures. This file is also available from the project homepage.

Format: ZIP Size: 4.8MB Download file

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Additional file 2:

This file contains a benchmark test of GenePainter on coronin (552 sequences, 1144 alignment positions), dynactin1 (207 sequences, 2112 alignment positions), dynactin3 (213 sequences, 428 alignment positions), Wiskott Aldrich Syndrome protein (229 sequences, 2051 alignment positions), and myosin heavy chain genes (2640 sequences, 9214 alignment positions). All sequences and gene structures can be found at CyMoBase (//www.cymobase.org).

Format: PDF Size: 55KB Download file

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Open Data