MOTIVATION Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the 'seed-and-extend' approach, in which occurrences of short subsequences called 'seeds' are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond ...

In the CoNLL 2003 NER shared task, more than two thirds of the submitted systems used a feature-rich representation of the task. Most of them used the maximum entropy principle to combine the features together. Others used large margin linear classifiers, such as SVM and RRM. In this paper, we compare several common classifiers under exactly the same conditions, demonstrating that the ranking o...

A variety of heterogenous data sources is available in the field of molecular biology. Our focus lies on the biological sequence data, i. e. data maintained in collections like EMBL or SWISS-PROT. We propose a relational model based on an Entity-Relationship approach for this discourse world. This is the foundation of a flexible architecture useful for a variety of purposes, e. g. for sequence ...

MOTIVATION Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments. A variety of theoretical foundations are being used to derive alignment-free methods that overcome this limitation. The formulation of alternative metrics for dissimilarity between sequences and their algo...

Abstract. A case of the matrix Kummer relation of Herz (1955) based on the Pearson VII type matrix model is derived in this paper. As a con- sequence, the polynomial Pearson VII configuration density is obtained and this sets the corresponding exact inference as a solvable aspect in shape theory. An application in postcode recognition, including a nu- merical comparison between the exact poly...

Word-based models have achieved promising results in sequence comparison. However, as the important statistical properties of words in biological sequence, how to use the overlapping structures and background information of the words to improve sequence comparison is still a problem. This paper proposed a new statistical method that integrates the overlapping structures and the background infor...

The well-known procedure implemented in ClustalW oriented on the sequence comparison was applied to structure comparison. The consensus sequence as well as consensus structure has been defined for proteins belonging to serpine family. The structure of early stage intermediate was the object for similarity search. The high values of W(sequence) appeared to be accordant with high values of W(stru...

A Bayesian analysis is used to detect a change-point in a sequence of independent random variables from exponential distributions. In This paper, we try to estimate change point which occurs in any sequence of independent exponential observations. The Bayes estimators are derived for change point, the rate of exponential distribution before shift and the rate of exponential distribution after s...