Spectral density ratio based clustering methods for the binary segmentation of protein sequences: A comparative study
Promponas, Vasilis J.
Google Scholar check
MetadataShow full item record
We compare several spectral domain based clustering methods for partitioning protein sequence data. The main instrument for this exercise is the spectral density ratio model, which specifies that the logarithmic ratio of two or more unknown spectral density functions has a parametric linear combination of cosines. Maximum likelihood inference is worked out in detail and it is shown that its output yields several distance measures among independent stationary time series. These similarity indices are suitable for clustering time series data based on their second order properties. Other spectral domain based distances are investigated as welland we compare all methods and distances to the problem of producing segmentations of bacterial outer membrane proteins consistent with their transmembrane topology. Protein sequences are transformed to time series data by employing numerical scales of physicochemical parameters. We also present interesting results on the prediction of transmembrane β-strands, based on the clustering outcome, for a representative set of bacterial outer membrane proteins with given three-dimensional structure. © 2010 Elsevier Ireland Ltd.
Showing items related by title, author, creator and subject.
Haploinsufficiency of the miR-873/miR-876 microRNA cluster is associated with craniofacial abnormalities Koufaris, Costas; Papagregoriou, Gregory N.; Kousoulidou, Ludmila; Moutafi, Maria; Tauber, Maïthé Thérèse; Jouret, Béatrice; Kieffer, Isabelle; Constantinou-Deltas, Constantinos D.; Tanteles, George A.; Anastasiadou, Violetta C.; Patsalis, Philippos C.; Sismani, Carolina (2015)MicroRNA haploinsufficiency has been associated with developmental defects in only a limited number of cases. Here we report a de novo genomic microdeletion that includes the LINGO2 gene as well as two microRNA genes, ...
Near full-length genetic analysis of HIV sequences derived from Cyprus: Evidence of a highly polyphyletic and evolving infection Kousiappa, Ioanna; Van De Vijver, D. A. M. C.; Kostrikis, Leontios G. (2009)The molecular epidemiology of HIV-1 infection was previously studied in Cyprus but the degree of HIV-1 diversity has remained indefinable. The main objective of the present study is to examine HIV-1 strains isolated from ...
Steps toward understanding the inheritance of repressive methyl-lysine marks in histones Reinberg, D.; Chuikov, S.; Farnham, P.; Karachentsev, D.; Kirmizis, Antonis; Kuzmichev, A.; Margueron, R.; Nishioka, K.; Preissner, T. S.; Sarma, K.; Abate-Shen, C.; Steward, R.; Vaquero, A. (2004)