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

BMC Bioinformatics

Software

Jeremy D Selengut¹  Daniel H Haft¹  Malay K Basu¹ 

[1] J. Craig Venter Institute, 20850, Rockville, MD, USA;

关键词: Protein Family;    Phylogenetic Profile;    Taxonomic Profile;    Query Profile;    Archaeal Methanogen;   

DOI  :  10.1186/1471-2105-12-434

 received in 2011-07-21, accepted in 2011-11-09,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundPhylogenetic 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.ResultsPartial 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.ConclusionProPhylo 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 ftp://ftp.jcvi.org/pub/data/ppp/.

【 授权许可】

CC BY   
© Basu et al; licensee BioMed Central Ltd. 2011