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222256.0 [No comment] 20.03.2013 11:45 Released

ID: 222256.0, MPI für Entwicklungsbiologie / Abteilung 1 - Protein Evolution (A. Lupas)
PhyloGenie: automated phylome generation and analysis.
Authors:Frickey, Tankred; Lupas, Andrei
Date of Publication (YYYY-MM-DD):2004-09-30
Title of Journal:Nucleic Acids Research
Journal Abbrev.:Nucleic Acids Res.
Issue / Number:17
Start Page:5231
End Page:5238
Sequence Number of Article:15459293
Review Status:not specified
Audience:Not Specified
Abstract / Description:Phylogenetic reconstruction is the method of choice to determine the homologous relationships between sequences. Difficulties in producing high-quality alignments, which are the basis of good trees, and in automating the analysis of trees have unfortunately limited the use of phylogenetic reconstruction methods to individual genes or gene families. Due to the large number of sequences involved, phylogenetic analyses of proteomes preclude manual steps and therefore require a high degree of automation in sequence selection, alignment, phylogenetic inference and analysis of the resulting set of trees. We present a set of programs that automates the steps from seed sequence to phylogeny and a utility to extract all phylogenies that match specific topological constraints from a database of trees. Two example applications that show the type of questions that can be answered by phylome analysis are provided. The generation and analysis of the Thermoplasma acidophilum phylome with regard to lateral gene transfer between Thermoplasmata and Sulfolobus, showed best BLAST hits to be far less reliable indicators of lateral transfer than the corresponding protein phylogenies.The generation and analysis of the Danio rerio phylome provided more than twice as many proteins as described previously, supporting the hypothesis of an additional round of genome duplication in the actinopterygian lineage.
External Publication Status:published
Document Type:Article
Affiliations:MPI für Entwicklungsbiologie/Abteilung 1 - Proteinevolution (Andrei Lupas)