Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural motifs in DNA sequences. Commonly used methods (e.g. MEME, Gibbs motif sampler) model binding sites as families of sequences described by a position weight matrix (PWM) and identify PWMs that maximize t...

We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM), reducing the influence of noise using a Principal Compo...

The binding affinity of DNA-binding proteins such as transcription factors is mainly determined by the base composition of the corresponding binding site on the DNA strand. Most proteins do not bind only a single sequence, but rather a set of sequences, which may be modeled by a sequence motif. Algorithms for de novo motif discovery differ in their promoter models, learning approaches, and othe...

The generation of genomic binding or accessibility data from massively parallel sequencing technologies such as ChIP-seq and DNase-seq continues to accelerate. Yet state-of-the-art computational approaches for the identification of DNA binding motifs often yield motifs of weak predictive power. Here we present a novel computational algorithm called MotifSpec, designed to find predictive motifs,...

MicroRNAs (miRNAs) are small regulatory molecules that repress the translational processes of their target genes by binding to their 3' untranslated regions (3' UTRs). Because the target genes are predominantly determined by their sequence complementarity to the miRNA seed regions (nucleotides 2-7) which are evolutionarily conserved, it is inferred that the target relationships and functions of...

MOTIVATION Many heuristic algorithms have been designed to approximate P-values of DNA motifs described by position weight matrices, for evaluating their statistical significance. They often significantly deviate from the true P-value by orders of magnitude. Exact P-value computation is needed for ranking the motifs. Furthermore, surprisingly, the complexity of the problem is unknown. RESULTS...

performances of electronic and mechanical draft control systems on a mf399 tractor were the objectives of the study to be evaluated and compared under field conditions. hence, the effects of two draft control systems (mechanical and electronic) under four ground speed levels and three set values of draft levels on rear wheel slippage, fuel consumption, compressive force within the top link and ...

Because of the increasing gap between the data from sequencing and structural genomics, the accurate prediction of the structural class of a protein domain solely from the primary sequence has remained a challenging problem in structural biology. Traditional sequence-based predictors generally select several sequence features and then feed them directly into a classification program to identify...

Each column of amino acids in a multiple alignment of protein sequences can be represented as a vector of 20 amino acid counts. For alignment and searching applications, the count vector is an imperfect representation of a position, because the observed sequences are an incomplete sample of the full set of related sequences. One general solution to this problem is to model unobserved sequences ...