Bioinformatics Advance Access published online on March 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm016
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PhyloGena – a user-friendly system for automated phylogenetic annotation of unknown sequences
1 Center for Computing Technologies (TZI), P.O.B. 330440, D-28334 Bremen, Germany, 2Urbanstr. 171B, D-10961 Berlin, 3Technology Transfer Centre (TTZ/BIBIS), An der Karlstadt 10, D-27568 Bremerhaven, Germany, and 4Alfred Wegener Institute, Am Handelshafen 12, D-27570 Bremerhaven, Germany
*To whom correspondence should be addressed. Dr. Klaus Valentin, E-mail: kvalentin{at}awi-bremerhaven.de
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Abstract |
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Motivation: Phylogenomic approaches towards functional and evolutionary annotation of unknown sequences have been suggested to be superior to those based only on pairwise local alignments. User-friendly sSoftware tools making the advantages of phylogenetic annotation available for the ever widening range of bioinformatically uninitiated biologists involved in genome / EST annotation projects are, however, not available. We were particularly confronted with this issue in the annotation of sequences from different groups of complex algae originating from secondary endosymbioses, where the identification of the phylogenetic origin of genes is often more problematic than in taxa well represented in the databases (e.g. animals, plants of fungi).
Results: We present a flexible pipeline with a user-friendly, interactive graphical user interface running on desktop computers that automatically performs a BLAST search of query sequences, selects a representative subset of them, then creates a multiple alignment from the selected sequences, and finally computes a phylogenetic tree. The pipeline, named PhyloGena, uses public domain software for all standard bioinformatics tasks (similarity search, multiple alignment, and phylogenetic reconstruction). As the major technological innovation, selection of a meaningful subset of BLAST hits was implemented using logic programming, modeled after the selection procedure as performed by human annotators. Results from the pipeline (BLAST tables, multiple alignments and phylogenetic trees) are displayed graphically, allowing the user to interact with the pipeline and deduce the function and phylogenetic origin of the query. PhyloGena thus makes phylogenomic annotation available also for those biologists without access to large computing facilities and with little informatics background. Although phylogenetic annotation is particularly useful when working with composite genomes (e.g., from complex algae), PhyloGena can be helpful in EST and genome annotation also in other organisms.
Availability: PhyloGena (executables for LINUX and Windows 2000/XP as well as source code) is available by anonymous ftp from http://awi.de/en/go/phylogena
Associate Editor: Dr. Chris Stoeckert
Received on October 13, 2006; revised on January 12, 2007; accepted on January 15, 2007
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