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Open Access Highly Accessed Methodology article

SynBlast: Assisting the analysis of conserved synteny information

Jörg Lehmann1*, Peter F Stadler12345 and Sonja J Prohaska456

Author Affiliations

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

2 Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany

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

4 Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA

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

6 Biomedical Informatics, Arizona State University, Tempe, PO-Box 878809, AZ 85287, USA

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BMC Bioinformatics 2008, 9:351  doi:10.1186/1471-2105-9-351

Published: 24 August 2008

Abstract

Motivation

In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information.

Results

Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. SynBlast uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how SynBlast is applied to retrieving orthologous and paralogous clusters using the vertebrate Hox and ParaHox clusters as examples.

Software

The SynBlast package written in Perl is available under the GNU General Public License at http://www.bioinf.uni-leipzig.de/Software/SynBlast/ webcite.