Open Access Research article

Genomic organization of eukaryotic tRNAs

Clara Bermudez-Santana12, Camille Stephan-Otto Attolini14, Toralf Kirsten1, Jan Engelhardt1, Sonja J Prohaska1, Stephan Steigele3 and Peter F Stadler15678*

Author Affiliations

1 Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany

2 Department of Biology, Universidad Nacional de Colombia. Carrera45 # 26-85 - Edificio Uriel Gutiérrez, Bogotá D.C., Colombia

3 Genedata AG Maulbeerstrasse 46 CH 4016 Basel, Switzerland

4 Biostatistics and Bioinformatics unit, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain

5 Max Planck Institute for Mathematics in the Sciences, Inselstraß 22 D-04103 Leipzig, Germany

6 Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany

7 Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA

8 Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria

For all author emails, please log on.

BMC Genomics 2010, 11:270  doi:10.1186/1471-2164-11-270

Published: 28 April 2010

Additional files

Additional file 1:

Genomic Distribution of tDNAs. Comprehensive overview of the genomic distribution of tRNA genes and tRNA pseudogenes as described in Fig. 1.

Format: PDF Size: 266KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Count of tDNAs and tDNA pair configurations. List of total tDNA predictions including P-values and counts of tDNA pair configurations from the empirical data and simulations.

Format: PDF Size: 178KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Co-occurrences of tDNAs. Comprehensive summary of co-occurrence data for tDNAs as described in Fig. 5.

Format: PDF Size: 224KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Syntenic conservation of Drosophila tDNAs. List of percentage distribution of tDNA synteny in the genus Drosophila.

Format: PDF Size: 17KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Sequence conservation of nematode tDNA-Ala. Neighbor-joining tree showing that tDNAs usually have identical sequences when they are syntenically conserved, while tRNAs with the same anticodon can exhibit small sequence variations within each species.

Format: PDF Size: 21KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Genome versions used in this survey. List of the genome versions and website from which they were downloaded.

Format: PDF Size: 190KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Proportions of tDNA pairs. Summary of the Fisher Test statistic for comparing proportion of pairs configurations.

Format: PDF Size: 170KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data