ARB: a software environment for sequence data

Wolfgang Ludwig

Oliver Strunk

Ralf Westram

Lothar Richter

Harald Meier

Yadhukumar Yadhukumar

Arno Buchner

Tina Lai

Susanne Steppi+23 authors

Lehrstuhl für Mikrobiologie, Technische Universität München, D-853530 Freising, Germany ^{Lehrstuhl für Rechnertechnik und Rechnerorganisation, Parallelrechnerarchitektur, Technische Universität München, D-85748 Garching, Germany}^{Institut für Informatik, Ruprecht-Karls-Universität Heidelberg, D-69120 Heidelberg, Germany}

^{To whom correspondence should be addressed. Tel: +8161 71 5451; Fax: +8161 71 5475; Email:}ed.nehcneum-ut.eigoloib.orkim@giwdul

Received 2004 Jan 13; Revised 2004 Jan 28; Accepted 2004 Jan 28.

Abstract

The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

Abstract

Datasets varying with respect to the number of sequence entries were used for PT server generation. The most comprehensive of these datasets comprising 25 743 entries and 40 000 alignment positions was used as a template for inserting the specified numbers of sequences into the database alignment or tree. For treeing, 2141 alignment columns were included.

ACKNOWLEDGEMENTS

The authors highly acknowledge F. O. Glöckner and R. Amann (Max Planck Institute for Marine Microbiology, Bremen, Germany) for redistributing the ARB database and software and answering user queries, as well as hosting and organizing ARB workshops. The authors thank Laura Schulz (Ludwig Maximilian University, Munich, Germany) for critical reading of the manuscript. ARB software development and database maintenance was partly supported by the European Union within the HRAMI project, by the German Research Foundation and by the German Ministry of Research and Education BIOLOG project.

ACKNOWLEDGEMENTS

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