EPPS: mining the COG database by an extended phylogenetic patterns search.
EPPS runs under Microsoft Windows. It is an extended version of the phylogenetic patterns search (PPS). The output condition of PPS is the exact match of a user defined phylogenetic pattern with the pattern represented by the respective cluster of orthologous groups (COG). In contrast, the software described here is less restrictive. The user may define the accuracy of the search by the number of genomes that are allowed not to match the predefined phylogenetic pattern. Thus, EPPS has the advantage to detect COGs even if organisms defined to be included are not or organisms defined to be excluded are present in the output COGs.
Reichard
Klaus
K
Institute of Mathematics, AG Statistics Institute of Neurobiochemistry, AG Proteinchemistry, University of Witten/Herdecke, Stockumer Str. 10, 58448 Witten, Germany.
Kaufmann
Michael
M
D000595:Amino Acid Sequence; D016000:Cluster Analysis; D017124:Conserved Sequence; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
D011506:Proteins