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

Hammesfahr, B., Odronitz, F., Mühlhausen, S., Waack, S., & Kollmar, M. (2013). GenePainter: A fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures. BMC Bioinformatics, 14: 77. doi:10.1186/1471-2105-14-77.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-F5E8-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-C834-3
Genre: Journal Article

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http://www.biomedcentral.com/1471-2105/14/77 (Publisher version)
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Hammesfahr, B.1, Author              
Odronitz, F.1, Author              
Mühlhausen, S.1, Author              
Waack, S., Author
Kollmar, M.1, Author              
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1Research Group of Systems Biology of Motor Protein, MPI for biophysical chemistry, Max Planck Society, ou_578570              

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 Abstract: Background: All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa. Results: GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol.

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Language(s): eng - English
 Dates: 2013-03-04
 Publication Status: Published online
 Pages: 11
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 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1186/1471-2105-14-77
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Title: BMC Bioinformatics
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Pages: - Volume / Issue: 14 Sequence Number: 77 Start / End Page: - Identifier: -