ProPhylo: Partial phylogenetic profiling to guide protein family construction and assignment of biological process

J. Craig Venter Institute, Rockville, MD 20850, USA.
BMC Bioinformatics (Impact Factor: 2.58). 11/2011; 12:434. DOI: 10.1186/1471-2105-12-434
Source: PubMed


Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies.
Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather than by relying on prebuilt protein families or fixed sequence similarity thresholds. Double Partial Phylogenetic Profiling (DPPP) is a related procedure that begins with a single sequence and searches for optimal granularities for its surrounding protein family in order to generate the best query profiles for PPP. We present ProPhylo, a high-performance software package for phylogenetic profiling studies through creating individually optimized protein family boundaries. ProPhylo provides precomputed databases for immediate use and tools for manipulating the taxonomic profiles used as queries.
ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from

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Available from: Jeremy Selengut, Sep 17, 2014
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    • "predicting protein-protein interactions and functional relationships such as in the PROLINKS and STRING servers [12]–[14]. Additionally, very recently a software package, ProPhylo, has been released designed to perform phylogenetic profiling studies [15]. ProPhylo addresses the major issue in such studies, that is reliably achieving granularities in similarity matrix required to obtain representative protein clusters. "
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    • "The result, a truth table of 1’s and 0’s for a large number of genomes, comprises a phylogenetic profile (19). The profile serves as input to the Partial Phylogenetic Profiling algorithm (20), which performs data mining to find (and guide construction of new HMMs for) additional protein families that belong to the same subsystem, even if the families in question have never before been defined and fall within large superfamilies. New models contribute to improved Genome Property definitions, more accurate comparative genomics, and iteratively improved descriptions of subsystems biology. "
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