Implicit motif distribution based hybrid computational kernel for sequence classification

Motivation: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive.


Estimation and hypothesis testing in BIB design and robustness
Tiku, Moti L.; ŞENOĞLU, BİRDAL (Elsevier BV, 2009-07-01)
Modified maximum likelihood estimators of the unknown parameters in a BIB design under non-normality of error distributions are obtained. They are shown to be more efficient and robust than the traditional least squares estimators. A test statistic for testing a linear contrast among treatment effects is developed. A real life example is given.
Estimation in bivariate nonnormal distributions with stochastic variance functions
Tiku, Moti L.; İslam, Muhammed Qamarul; SAZAK, HAKAN SAVAŞ (Elsevier BV, 2008-01-01)
Data sets in numerous areas of application can be modelled by symmetric bivariate nonnormal distributions. Estimation of parameters in such situations is considered when the mean and variance of one variable is a linear and a positive function of the other variable. This is typically true of bivariate t distribution. The resulting estimators are found to be remarkably efficient. Hypothesis testing procedures are developed and shown to be robust and powerful. Real life examples are given.
Manguoğlu, Murat; Sameh, Ahmed H.; Grama, Ananth (Society for Industrial & Applied Mathematics (SIAM), 2010-01-01)
The emergence of multicore architectures and highly scalable platforms motivates the development of novel algorithms and techniques that emphasize concurrency and are tolerant of deep memory hierarchies, as opposed to minimizing raw FLOP counts. While direct solvers are reliable, they are often slow and memory-intensive for large problems. Iterative solvers, on the other hand, are more efficient but, in the absence of robust preconditioners, lack reliability. While preconditioners based on incomplete factor...
Joint linear complexity of multisequences consisting of linear recurring sequences
Fu, Fang-Wei; Niederreiter, Harald; Özbudak, Ferruh (Springer Science and Business Media LLC, 2009-04-01)
The linear complexity of sequences is one of the important security measures for stream cipher systems. Recently, in the study of vectorized stream cipher systems, the joint linear complexity of multisequences has been investigated. In this paper, we study the joint linear complexity of multisequences consisting of linear recurring sequences. The expectation and variance of the joint linear complexity of random multisequences consisting of linear recurring sequences are determined. These results extend the ...
Integrated search and alignment of protein structures
Sacan, Ahmet; Toroslu, İsmail Hakkı; Ferhatosmanoglu, Hakan (Oxford University Press (OUP), 2008-12-15)
Motivation: Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The ...
Citation Formats
M. V. Atalay, “Implicit motif distribution based hybrid computational kernel for sequence classification,” BIOINFORMATICS, pp. 1429–1436, 2005, Accessed: 00, 2020. [Online]. Available: